From lindahl at stanford.edu  Fri Aug  1 00:59:00 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Fri Aug  1 00:59:00 2003
Subject: [gmx-users] benchmarking results
In-Reply-To: <20030731204704.35166.qmail@web40712.mail.yahoo.com>
Message-ID: <67A9E751-C3AA-11D7-A210-000A95A099E0@stanford.edu>

On Thursday, July 31, 2003, at 01:47 PM, Crystal Hancock wrote:

> To whom it may concern:
>  I have a question in regards to a table on the
> gromacs website. There is a table located at the
> bottom of the page at
> http://www.gromacs.org/benchmarks/single.php. I shows
> the machine, cpu, clock, cache, and the a number for
> each benchmark (villin, lys/cut, lys/PME, DPPC,
> Poly-CH2). However, there is nowhere that says what
> this number represents. Is it time? Mflops? If anyone
> knows, please let me know. I would like to compare my
> results with these, but I'm not sure what to look at
> to compare.

Hi Crystal,

I'm pretty sure it says somewhere on the page, but the unit is 
picoseconds of simulation per day (i.e. 24h). At the end of a 
simulation Gromacs prints the performance per hour - just multiply that 
by 24.

Cheers,

Erik



From ygmu at theochem.uni-frankfurt.de  Fri Aug  1 08:31:02 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Fri Aug  1 08:31:02 2003
Subject: [gmx-users] graphite
In-Reply-To: <1059644105.27733.7.camel@werkman.bmc.uu.se>
Message-ID: <Pine.LNX.4.44.0308010829310.9016-100000@marge.theochem.uni-frankfurt.de>

I encounter such error message :
There were 2 inconsistent shifts. Check your topology

What does it mean ?


Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711




From spoel at xray.bmc.uu.se  Fri Aug  1 09:38:00 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Fri Aug  1 09:38:00 2003
Subject: [gmx-users] Simulated annealing (now genbox)
In-Reply-To: <20030731212806.35914.qmail@web21511.mail.yahoo.com>
References: <20030731212806.35914.qmail@web21511.mail.yahoo.com>
Message-ID: <1059723320.30089.1.camel@werkman.bmc.uu.se>

On Thu, 2003-07-31 at 23:28, Albert Sun wrote:
> How can we use other molecules to replace protein and solvent when
> using genbox?
> could we use other .gro files to replace protein.gro and spc216.gro ? 
yes, the only restriction is that the solvent should be one residue per
molecule. e.g. dmso.gro could be used. You can also use mixed solvent,
i.e. you can start with an equilibrated water/methanol box and solvate
your protein in that.
>   
>  
>  
>  
>  
>    
> Osmany Guirola Cruz <osmany.guirola at cigb.edu.cu> wrote:
>         Thanks Xaviier
>         
>         
>         Xavier Periole wrote:
>         >  
>         >         
>         >         1) How can i use genbox to insert extramolecules of
>         >         solvent?
>         >         
>         >         
>         >          
>         > a simple genbox -h gives you the answer. But basically
>         > something like :
>         >  
>         > genbox -cp protein.gro -cs spc216.gro -nmol <number of
>         > molecules you want> 
>         >             -try ......
>         >  
>         > take a look.
>         >  
>         > XAvier
>         >  
>         >  
>         
> 
> 
> ______________________________________________________________________
> Do you Yahoo!?
> Yahoo! SiteBuilder - Free, easy-to-use web site design software
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From feenstra at chem.vu.nl  Fri Aug  1 09:43:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Fri Aug  1 09:43:01 2003
Subject: [gmx-users] Langevin dynamics
In-Reply-To: <001301c35722$78bea350$341e738c@folding>
References: <000001c355d3$01d5e000$c47b14c8@HELIO> <3F269492.2020000@chem.vu.nl> <001301c35722$78bea350$341e738c@folding>
Message-ID: <3F293814.80703@chem.vu.nl>

Jia-Lin Lo wrote:
> Hi;
>      I would like to know how do you perform LD with not explicit solvent.
> Did gromacs provide implict solvent model? If not, how did you simulate
> the protein with LD method.  How did you make gro and top files.
> Thanks in advance.

I never used LD, but Berk Hess (my roommate then, reads this list too) did.
AFAIR, he only used distance dependent dielectric. There are rumours
about an implicit solvent model bein implemented in Vijay Pande's group
(Stanford U, for the folding at home project), but AFAIK it hasn't been
released (yet).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Fri Aug  1 09:43:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Fri Aug  1 09:43:01 2003
Subject: [gmx-users] back calculation of NOE:s
In-Reply-To: <1059644481.27733.14.camel@werkman.bmc.uu.se>
References: <ICEELOGDPMLPEIBKCFFBKEPKCCAA.jonas.fast@bpc.lu.se> <1059644481.27733.14.camel@werkman.bmc.uu.se>
Message-ID: <3F293C57.3080208@chem.vu.nl>

David van der Spoel wrote:
> On Thu, 2003-07-31 at 11:43, Jonas Fast wrote:
>>As a beginner with gromacs and structure calculations, I have used gromacs
>>to get the structure of a protein bound fatty acid from NOE data (only using
>>the internal fatty acid NOE:s to get distance restraints). Now I would like
>>to check the result by back calculating a noesy spectra. Could somebody line
>>up a feasible pathway for that together with suitable software tips. I am at
>>the state where I have made a successful (?) full MD simulation of the
>>system (fa, water and sodium as a counter ion).
> 
> this is an interesting topic. You may consider to use experimental
> chemical shifts, because calculated ones are not accurate enough,
> however it would also be interesting to compute chemical shifts (using
> David Case's programs) and then build up a spectrum like that. The
> intensity of the NOE's is proportional to 
> sigma = r^6

Well, only to a rather crude approximation. If you already have the simulations,
you can do much better by taking the proton pair spectral density functions
from the distance (auto)correlations, and then integrate the relaxation matrix
to the appropriate mixing time. If you're still with me, you may want to read
some of Christine Peter's papers (Wilfred van Gunsteren's group , ETH Zurich).
She also analyzed some of my peptide simulations, so I could compare them to
my NMR experiments. The corresponding paper is: J. Biomol. NMR 23, 181-194, 2002
(there is a .pdf of it on my homepage at http://www.few.vu.nl/~feenstra/ ).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From alan at biof.ufrj.br  Fri Aug  1 14:00:01 2003
From: alan at biof.ufrj.br (Alan Wilter Sousa da Silva)
Date: Fri Aug  1 14:00:01 2003
Subject: [gmx-users] Langevin dynamics
In-Reply-To: <3F293814.80703@chem.vu.nl>
References: <000001c355d3$01d5e000$c47b14c8@HELIO> <3F269492.2020000@chem.vu.nl>
 <001301c35722$78bea350$341e738c@folding> <3F293814.80703@chem.vu.nl>
Message-ID: <Pine.LNX.4.53.0308010843190.21149@iracema.biof.ufrj.br>

I used LD but not in GMX.  The idea I employed is something like that:

A had a protein complexed with a substrate.  I want solvent, but my
box system created is very big.  So, I take a sphere embracing my whole
protein system with all solvent that can fit in and apply LD to a spheric
section region, lessing a smaller interior sphere under classic MD.
Moreover, the atoms under LD must be position restrained. Then, all 
atoms outside the exterior sphere are removed.

I don't know if GMX is able to do it, since it will involve a radical 
modification in topologies files.

See reference below for further details:

Stochastic molecular dynamics of peanut lectin PNA complex with T-antigen
disaccharide
 Caffarena ER, Grigera JR, Bisch PM
 JOURNAL OF MOLECULAR GRAPHICS & MODELLING 21 (3): 227-240 DEC 2002
 
Cheers,

On Thu, 31 Jul 2003, Anton Feenstra wrote:

> Jia-Lin Lo wrote:
> > Hi;
> >      I would like to know how do you perform LD with not explicit solvent.
> > Did gromacs provide implict solvent model? If not, how did you simulate
> > the protein with LD method.  How did you make gro and top files.
> > Thanks in advance.
> 
> I never used LD, but Berk Hess (my roommate then, reads this list too) did.
> AFAIR, he only used distance dependent dielectric. There are rumours
> about an implicit solvent model bein implemented in Vijay Pande's group
> (Stanford U, for the folding at home project), but AFAIK it hasn't been
> released (yet).
> 
> 
> 

-- 
-----------------------
Alan Wilter S. da Silva
-----------------------
 Laborat?rio de F?sica Biol?gica
  Instituto de Biof?sica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil


From paloureiro at biof.ufrj.br  Fri Aug  1 20:31:01 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Fri Aug  1 20:31:01 2003
Subject: [gmx-users] 1-4 LJ parameters for OW
Message-ID: <1059762428.3f2ab0fc426da@webmail.biof.ufrj.br>

Dear users,

I hope this is not a stupid question, but why does one need 1-4 LJ interactions
for OW (water oxygen)?

Cheers,

Pedro. 

--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil 


From lindahl at stanford.edu  Fri Aug  1 21:10:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Fri Aug  1 21:10:01 2003
Subject: [gmx-users] 1-4 LJ parameters for OW
In-Reply-To: <1059762428.3f2ab0fc426da@webmail.biof.ufrj.br>
Message-ID: <947DEB08-C453-11D7-B59D-000A95A099E0@stanford.edu>

On Friday, August 1, 2003, at 11:27 AM, Pedro Alexandre Lapido Loureiro 
wrote:

> Dear users,
>
> I hope this is not a stupid question, but why does one need 1-4 LJ 
> interactions
> for OW (water oxygen)?
>
Hi Pedro,

You don't, but they were probably generated automatically by some 
script for all atoms in the forcefield :-)

Cheers,

Erik



From albert_sun9 at yahoo.com  Fri Aug  1 23:42:01 2003
From: albert_sun9 at yahoo.com (Albert Sun)
Date: Fri Aug  1 23:42:01 2003
Subject: [gmx-users] Re: Inquiry Again.
In-Reply-To: <3F26532F.1000709@chem.vu.nl>
Message-ID: <20030801214131.762.qmail@web21512.mail.yahoo.com>

Dear Anton and Gmx-users,
 
If without bonds, I think the top file (as shown in urea.top - manual page 100) will like this:
[moleculetype]
;name   nrexcl
Urea        3
 
[atom]
;nr      type
1    C
2    O
3    NT
4    H
..
 
[bonds]  ; no need to input
 
[pairs]
;ai       aj        funct           b0       kb
  3       4         1            1.0e-01    3.74468e+05
  3       5         1            1.0e-01    3.74468e+05
  ...
 
[angles]  ;  no need to input
 
[dihedrals];  no need to input
 
[position_restraints}
1    1    1000     1000    10000
...
 
 
;include SPC water topology
#include  "spc.itp"
 
[system]
Urea in water
 
[molecules]
Urea          1
Sol            1000
 
Appreciate if you could correct it if any mistakes.
Besides, how could we select ' without bonds'  when we do pdb2gmx or by modifying 
.pdb file ?
 
 
Thanks in advance.
 
Albert


Anton Feenstra <feenstra at chem.vu.nl> wrote:
Victor Kowalenko wrote:
> Hi Anton,
> 
> I am sending you this e-mail to confirm that the following is all
> I need to get our atomic modelling working in GROMACS as I am not entirely
> sure that this will work.
> 
> First, I need to write a script file that will create *.top file from the
> pdb files. I should mention the format of our pdb files just in case their
> format is unsuitable for GROMACS. They basically go like this:

Whether you need a script depends if you want bonds, without bonds the
.top will be rather trivial and can be written by hand.

> HETATM 

x y z 0.00 0.00 
> e.g.
> HETATM 1 Al Al 1 0 0 0 0.00 0.00 Al
> HETATM 2 Cu Cu 2 0 0 1 0.00 0.00 Cu
> etc.
> 
> I think the zeros correspond to velocities or some other units, but they
> are irrelevant for the time being. It is x, y and z coordinates that are 
> important. I would like to know if this format is suitable for GROMACS or
> whether I need to write a script file that extracts only the coordinates.
> The files will have to be altered anyway as the coordinate positions are
> in Angstroms while there is a preference for nm in GROMACS.

Close, but not quite there... This looks like the general .pdb format anyway.
The zeroes should be occupancy and B-factor. Irrelevant for us. The units in
Gromacs files are nm, but .pdb is not a Gromacs file format and the official
PDB file format description insists on angstroms. So, in .pdb you must use
Angtroms, and in .gro nm. It looks like Gromacs will read your files just fine.

> As far as the topology file is concerned, it appears to me that if I elect 
> only to do atom interactions I only need to create a script file that
> creates a topology file with only 2 main parts to it: [atomtypes] and
> [atoms]. That is, it should look like:
> 
> [atomtypes]
> ; specify the various types of atoms in the simulation
> ; atom atomic mass charge epsilon sigma
> Al 26.98 0 LJ_energy in kJ/mol LJ_radius in nm
> Cu 63 0 LJ_energy_2 in kJ/mol LJ_radius_2 in nm
> [atoms]
> ; nr atom type
> 1 Al
> 2 Cu
> 3 Al
> etc.
> 
> where the numbers in the [atoms] correspond to the numbers in the pdb
> files so that GROMACS can get the particle coordinates. 
> 
> I think this is what you are saying below and if this is correct, then
> I see no problem in writing a little script file to read the pdb file
> a structure file. Please inform me as to whether this is correct or
> whether I have missed something. My aim is to create a general script
> file that will variable numbers of particles in the pdb files and place
> them in this format. If the pdb format is no good, then I could create a
> new pdb file with the proper format. 
> 
> Cheers,
> Victor.

Sounds good. You did not include all the obligatory sections above in
your 'example' .top, check the manual for the complete description of
the .top file format.


-- 
Groetjes,

Anton
_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
|_____________|_______________________________________________________|


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From PNAGY at UTNet.UToledo.Edu  Sat Aug  2 01:52:00 2003
From: PNAGY at UTNet.UToledo.Edu (Nagy, Peter I.)
Date: Sat Aug  2 01:52:00 2003
Subject: [gmx-users] disulfide bond
Message-ID: <B16CE043598D02408DC7DE5A36B2767C0AA5A7@msgdb01.utad.utoledo.edu>

Dear Gromacs Users!

   I created a pdb file for a protein in Sybyl, where I had a disulfide bond.
Sybyl distinguished these two residues by CYX as compared to the regular CYS.
   When I used pdb2gmx, the system complained about CYX and responded that
tries to consider these residues as CYS2. It was fine, but in the conf.gro and topol.top files I noticed that the backbone H (to N) was not generated.
Furthermore, the S-S bond was not generated in the topol.top file.
   Perhaps I could edit this latter file by following the topology and charge
parameters for a backbone H(N), but I do not have its coordinates in the conf.gro. I am sure that there is a simple way to handle the S-S in Gromacs.
   What should I modify in the original .pdf file to get correct .gro and
.top files?

Thanks, Peter Nagy
pnagy at utnet.utoledo.edu
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From mceruso at physbio.mssm.edu  Sat Aug  2 01:57:01 2003
From: mceruso at physbio.mssm.edu (Marc Ceruso)
Date: Sat Aug  2 01:57:01 2003
Subject: [gmx-users] disulfide bond
References: <B16CE043598D02408DC7DE5A36B2767C0AA5A7@msgdb01.utad.utoledo.edu>
Message-ID: <000901c35888$71bfd620$8d03cb92@CUAUHNAHUAC>

disulfide bondTry renaming CYX to CYS, pdb2gmx should find the disulfide bond by itself.

marc
  ----- Original Message ----- 
  From: Nagy, Peter I. 
  To: gmx-users at gromacs.org 
  Sent: Friday, August 01, 2003 7:51 PM
  Subject: [gmx-users] disulfide bond


  Dear Gromacs Users!

     I created a pdb file for a protein in Sybyl, where I had a disulfide bond.
  Sybyl distinguished these two residues by CYX as compared to the regular CYS.
     When I used pdb2gmx, the system complained about CYX and responded that
  tries to consider these residues as CYS2. It was fine, but in the conf.gro and topol.top files I noticed that the backbone H (to N) was not generated.
  Furthermore, the S-S bond was not generated in the topol.top file.
     Perhaps I could edit this latter file by following the topology and charge
  parameters for a backbone H(N), but I do not have its coordinates in the conf.gro. I am sure that there is a simple way to handle the S-S in Gromacs.
     What should I modify in the original .pdf file to get correct .gro and
  .top files?

  Thanks, Peter Nagy
  pnagy at utnet.utoledo.edu 
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From nanyu101 at sina.com  Sat Aug  2 10:13:01 2003
From: nanyu101 at sina.com (nanyu101)
Date: Sat Aug  2 10:13:01 2003
Subject: [gmx-users] how to set up an electric fields!!!!!!
Message-ID: <20030802081232.15320.qmail@sina.com>

Dear gmx-users,
  I want to set up an electric field for my ion channel in the lipid bilayer.Would you please tell me how to set up it?

I have failed doing this.
E_x = 1.0 
E_y = 0.5
E_z = 2.0

Any comment is appreciated.

Best wishes,
nanyu
______________________________________
Best wishes,
Xianhui Wu
===================================================================
????9???????????????????????? (http://mail.sina.com.cn)


From dastmalchi.s at tbzmed.ac.ir  Sun Aug  3 10:40:01 2003
From: dastmalchi.s at tbzmed.ac.ir (Dastmalchi)
Date: Sun Aug  3 10:40:01 2003
Subject: [gmx-users] Drug - Enzyme tutorial
Message-ID: <003201c3599a$a80a2a60$6480a8c0@dasmalchi>

Dear Collegues,

I am new to GROMACS, and was going through the Drug-Enzyme tutorial. I am using CROMACS on a PC running WinXP. When I issue the following command "genbox -cp trp.gro -cs spc216.gro -o trp_b4em.gro -p trp.top", I get an empty trp.top file. I tried to edit the top file using temp.top and did many other thing to continue the tutorial but it didn't work. I was wondering if you could kindly help me out with this.

Cheers, Siavoush
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From dastmalchi.s at tbzmed.ac.ir  Sun Aug  3 16:57:01 2003
From: dastmalchi.s at tbzmed.ac.ir (Dastmalchi)
Date: Sun Aug  3 16:57:01 2003
Subject: [gmx-users] topology file
Message-ID: <00bb01c359cf$6a41b7e0$6480a8c0@dasmalchi>

Dear colleagues,

Is there any way to make topology files for some except the ProGrg server. I am dealing with cofactors, molybdenum and Fe2S2 molecules and would like to include them in the modeling of an enzyme.
Many thanks for you kind attentions.

Cheers, Siavoush
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From jayant_jacques at rediffmail.com  Sun Aug  3 19:54:00 2003
From: jayant_jacques at rediffmail.com (Jayant James Jayasundar)
Date: Sun Aug  3 19:54:00 2003
Subject: [gmx-users] (no subject)
Message-ID: <20030803175428.9854.qmail@webmail6.rediffmail.com>

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From spoel at xray.bmc.uu.se  Sun Aug  3 20:09:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Sun Aug  3 20:09:01 2003
Subject: [gmx-users] (no subject)
In-Reply-To: <20030803175428.9854.qmail@webmail6.rediffmail.com>
References: <20030803175428.9854.qmail@webmail6.rediffmail.com>
Message-ID: <1059934381.1743.7.camel@h28n2fls34o1123.telia.com>

On Sun, 2003-08-03 at 19:54, Jayant James Jayasundar wrote:
> hi all,
> I was just wondering how the protonation states of Histidines are 
> assigned by gromacs? For some histidines with low solvent 
> accessibility (found by means of WHATIF) the Histidines are 
> assigned a protonation state of HISB (accessibility is less than 
> 2.0) but for an accessibility of 24.9014 the histidine is assigned 
> a state HISB and for an accessibility of 19.305 the histidine is 
> assigned a state HISA then a histidine with accessibility 4.1372 
> the state assigned is HISH by gromacs  on what basis is the 
> assignments made as I am trying to do some pH based MD work??
First off all you can fully control protonation manually with the -inter
flag to pdb2gmx, and some more flags. Furthermore pdb2gmx computes the
hydrogen bonding pattern in the protein, and if there is indication that
the proton should be on the NE2 rather than ND1 it is put there.
Default  (in solution) is ND1. Doubly protonated is possible but depends
again on your hbonding pattern. If you  runpdb2gmx -debug the complete
list of hbonds will be dumped in pdb2gmx.log

> Regs
> Jayant
> 
> 
> Jayasundar Jayant James
> Research scholar
> Centre for Biotechnology
> Anna University. Chennai - 600 025.INDIA
> Ph 2350772(Office), Cell-9841042164,
> Res 4935864
> ___________________________________________________
> Download the hottest & happening ringtones here!
> OR SMS: Top tone to 7333
> Click here now: 
> http://sms.rediff.com/cgi-bin/ringtone/ringhome.pl
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From feenstra at chem.vu.nl  Mon Aug  4 08:47:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug  4 08:47:01 2003
Subject: [gmx-users] Langevin dynamics
In-Reply-To: <Pine.LNX.4.53.0308010843190.21149@iracema.biof.ufrj.br>
References: <000001c355d3$01d5e000$c47b14c8@HELIO> <3F269492.2020000@chem.vu.nl> <001301c35722$78bea350$341e738c@folding> <3F293814.80703@chem.vu.nl> <Pine.LNX.4.53.0308010843190.21149@iracema.biof.ufrj.br>
Message-ID: <3F2A91BF.9090604@chem.vu.nl>

Alan Wilter Sousa da Silva wrote:
> I used LD but not in GMX.  The idea I employed is something like that:
> 
> A had a protein complexed with a substrate.  I want solvent, but my
> box system created is very big.  So, I take a sphere embracing my whole
> protein system with all solvent that can fit in and apply LD to a spheric
> section region, lessing a smaller interior sphere under classic MD.
> Moreover, the atoms under LD must be position restrained. Then, all 
> atoms outside the exterior sphere are removed.
> 
> I don't know if GMX is able to do it, since it will involve a radical 
> modification in topologies files.

No, combination of LD and MD is not implemented. Seeing that a QM/MM
approach has been implemented (partially, and not nearly release-ready,
and not by me), it may be an idea to have something like 'integrator'
groups, where arbitrary selections of molecules could be handled by
different integrators (i.e., MD, LD, QM, whatever). There does need to
be some arrangement for the border area between integrators, though.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From yesint4 at yahoo.com  Mon Aug  4 09:10:02 2003
From: yesint4 at yahoo.com (Semen Esilevsky)
Date: Mon Aug  4 09:10:02 2003
Subject: [gmx-users] Where to find Gromacs 3.1.5?
In-Reply-To: <1059609891.3f285d2366979@webmail.utoronto.ca>
Message-ID: <20030804070901.94225.qmail@web40502.mail.yahoo.com>

Dear all,
where can I find Gromacs 3.1.5? I didn't found it on
the official site...

Sincerely,
Semen


__________________________________
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
http://sitebuilder.yahoo.com


From spoel at xray.bmc.uu.se  Mon Aug  4 09:26:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Mon Aug  4 09:26:01 2003
Subject: [gmx-users] Where to find Gromacs 3.1.5?
In-Reply-To: <20030804070901.94225.qmail@web40502.mail.yahoo.com>
References: <20030804070901.94225.qmail@web40502.mail.yahoo.com>
Message-ID: <1059982160.12991.1.camel@h28n2fls34o1123.telia.com>

On Mon, 2003-08-04 at 09:09, Semen Esilevsky wrote:
> Dear all,
> where can I find Gromacs 3.1.5? I didn't found it on
> the official site...
> 
> Sincerely,
> Semen

It's not there yet.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From Vojtech.Spiwok at vscht.cz  Mon Aug  4 11:45:01 2003
From: Vojtech.Spiwok at vscht.cz (=?iso-8859-2?Q?Ing._Vojt=ECch_Spiwok?=)
Date: Mon Aug  4 11:45:01 2003
Subject: [gmx-users] RE:  Drug - Enzyme tutorial (Dastmalchi)
References: <20030803100001.32500.87519.Mailman@hawk.theophys.kth.se>
Message-ID: <00bf01c35a6c$fc49ab00$39782193@vscht.cz>

> Dear Collegues,
> 
> I am new to GROMACS, and was going through the Drug-Enzyme tutorial. I
> am using CROMACS on a PC running WinXP. When I issue the following 
> command "genbox -cp trp.gro -cs spc216.gro -o trp_b4em.gro -p trp.top", 
> I get an empty trp.top file. I tried to edit the top file using temp.top 
> and did many other thing to continue the tutorial but it didn't work. I 
> was wondering if you could kindly help me out with this.
> 
> Cheers, Siavoush
Dear Siavoush
It must be bug or compiling error. Delete the empty trp.top file and rename
temp.top (or whatever is the name of the top file created by genbox) to
trp.top and it should work. Or instal Linux on your machine.

Sincerely
Vojtech Spiwok
ICT Prague




From kay.gottschalk at weizmann.ac.il  Mon Aug  4 11:57:01 2003
From: kay.gottschalk at weizmann.ac.il (Kay Gottschalk)
Date: Mon Aug  4 11:57:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <1059506049.3f26c7819e757@webmail.huji.ac.il>
Message-ID: <DB290E8C-C661-11D7-B092-000393BB411E@weizmann.ac.il>

Hi all,

does anyone know how to use g_rdf angle-dependent? In the manual it's 
written that one can define some angle theta (which affects the 
averaging), but somehow I can't figure out how to define that angle.
Thanks for your help,
Kay.



From spoel at xray.bmc.uu.se  Mon Aug  4 12:26:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Mon Aug  4 12:26:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <DB290E8C-C661-11D7-B092-000393BB411E@weizmann.ac.il>
References: <DB290E8C-C661-11D7-B092-000393BB411E@weizmann.ac.il>
Message-ID: <1059993009.12989.25.camel@h28n2fls34o1123.telia.com>

On Mon, 2003-08-04 at 11:56, Kay Gottschalk wrote:
> Hi all,
> 
> does anyone know how to use g_rdf angle-dependent? In the manual it's 
> written that one can define some angle theta (which affects the 
> averaging), but somehow I can't figure out how to define that angle.
> Thanks for your help,
> Kay.
> 
I think that option has been lost a long while ago...


> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From jxs818 at bham.ac.uk  Mon Aug  4 12:35:01 2003
From: jxs818 at bham.ac.uk (jxs818 at bham.ac.uk)
Date: Mon Aug  4 12:35:01 2003
Subject: [gmx-users] cpp and SGI irix 6.5
Message-ID: <E19jcfD-0000tE-00@www.bham.ac.uk>

Hi All, 
I have compiled gromacs on an SGI irix 6.5, but there is no 
CPP on the system. Where can i download a copy (GPL).
Many thanks in advance
John 




From spoel at xray.bmc.uu.se  Mon Aug  4 12:57:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Mon Aug  4 12:57:01 2003
Subject: [gmx-users] cpp and SGI irix 6.5
In-Reply-To: <E19jcfD-0000tE-00@www.bham.ac.uk>
References: <E19jcfD-0000tE-00@www.bham.ac.uk>
Message-ID: <1059994861.12989.28.camel@h28n2fls34o1123.telia.com>

On Mon, 2003-08-04 at 12:34, jxs818 at bham.ac.uk wrote:
> Hi All, 
> I have compiled gromacs on an SGI irix 6.5, but there is no 
> CPP on the system. Where can i download a copy (GPL).

You can find something called freeware on the SGI website. That has
amongst other the gcc compiler. You could check whether it is not yet
installed in your system, default directory would be /usr/freeware

> Many thanks in advance
> John 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From kay.gottschalk at weizmann.ac.il  Mon Aug  4 14:55:01 2003
From: kay.gottschalk at weizmann.ac.il (Kay Gottschalk)
Date: Mon Aug  4 14:55:01 2003
Subject: [gmx-users] g_rdf
Message-ID: <CB15B34C-C67A-11D7-B092-000393BB411E@weizmann.ac.il>

Hi all,

does anyone know how to use g_rdf angle-dependent? In the manual it's 
written that one can define some angle theta (which affects the 
averaging), but somehow I can't figure out how to define that angle.
Thanks for your help,
Kay.



From kay.gottschalk at weizmann.ac.il  Mon Aug  4 15:01:01 2003
From: kay.gottschalk at weizmann.ac.il (Kay Gottschalk)
Date: Mon Aug  4 15:01:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <1059993009.12989.25.camel@h28n2fls34o1123.telia.com>
Message-ID: <A297185C-C67B-11D7-B092-000393BB411E@weizmann.ac.il>

Hmm, too bad. Any idea how to do the averaging then? If I want to  
calculate the rdf of solvent around a certain surface atom, I will have  
to compensate for volume of the protein, I think. I am not really sure  
how to do that...
Thanks,
Kay.
On Monday, August 4, 2003, at 01:30 PM, David wrote:

> On Mon, 2003-08-04 at 11:56, Kay Gottschalk wrote:
>> Hi all,
>>
>> does anyone know how to use g_rdf angle-dependent? In the manual it's
>> written that one can define some angle theta (which affects the
>> averaging), but somehow I can't figure out how to define that angle.
>> Thanks for your help,
>> Kay.
>>
> I think that option has been lost a long while ago...
>
>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> --  
> Groeten, David.
> _______________________________________________________________________ 
> _
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> +
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel



From asaraujo at if.sc.usp.br  Mon Aug  4 16:21:01 2003
From: asaraujo at if.sc.usp.br (Alexandre Suman de Araujo)
Date: Mon Aug  4 16:21:01 2003
Subject: [gmx-users] Mpi version of GROMACS - Doubt about its performance
Message-ID: <3F2E6EB2.8040707@if.sc.usp.br>

Hi GMXer

I have a 4 nodes beowulf cluster and I installed de MPI version of 
GROMACS in it. To make a test I performed the same simulation in the 4 
nodes and after in only one node.
The  total time of simulation using the 4 nodes was only 10% faster than 
using only 1 node. This is correct???? Or somebody has a better performance?
The ethernet interface between the node is a 100Mb/s one... I think this 
is enough... or not???
Waiting coments.

Best Regards.

-- 
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - S?o Carlos - Brasil




From hsu at panda.chem.uu.nl  Mon Aug  4 16:49:00 2003
From: hsu at panda.chem.uu.nl (Shang-Te Danny Hsu)
Date: Mon Aug  4 16:49:00 2003
Subject: [gmx-users] Mpi version of GROMACS - Doubt about its performance
References: <3F2E6EB2.8040707@if.sc.usp.br>
Message-ID: <3F2E725D.2010208@nmr.chem.uu.nl>

Dear Alexandre,

We also noticed the same problem with our SuSE8.1 Linux cluster with 
mpich-1.2.1 and 1Gb/s ethernet interface. It only used less then 5% CPU 
that was available when the parallel jobs were distributed 
automatically. So far we found two temporary solutions:

1. Resubmit your parallel jobs repeatedly until it runs properly 
(normally the third time it becomes okay)

2. Manually define the machines you'd like to distribute your jobs to.

We are still testing other possibilities

Cheers,
Danny

Alexandre Suman de Araujo wrote:
> Hi GMXer
> 
> I have a 4 nodes beowulf cluster and I installed de MPI version of 
> GROMACS in it. To make a test I performed the same simulation in the 4 
> nodes and after in only one node.
> The  total time of simulation using the 4 nodes was only 10% faster than 
> using only 1 node. This is correct???? Or somebody has a better 
> performance?
> The ethernet interface between the node is a 100Mb/s one... I think this 
> is enough... or not???
> Waiting coments.
> 
> Best Regards.
> 


-- 
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl



From tccf at epq.ime.eb.br  Mon Aug  4 17:21:02 2003
From: tccf at epq.ime.eb.br (Tanos)
Date: Mon Aug  4 17:21:02 2003
Subject: [gmx-users] Calculation stopping
Message-ID: <002101c35a9b$e9b3a0c0$c47b14c8@HELIO>

            Hi folks, 
            Lately I have faced a very strange problem when using
GROMACS: My MD calculations stop without any apparent reason. I am
trying 100 ps of MD in a system of 130.000 atoms, but when calculation
reaches about step 25000, it suddenly stops without any error message.
The files .job and .log remain unchanged as the calculation was yet on.
Does someone has any idea of what can be happening ???????? 
            Thanks in advance.
            Tanos C. C. Franca
            IME ? Rio de Janeiro - Brazil

---
Outgoing mail is certified Virus Free.
Checked by AVG anti-virus system (http://www.grisoft.com).
Version: 6.0.504 / Virus Database: 302 - Release Date: 24/07/2003
 
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From asaraujo at if.sc.usp.br  Mon Aug  4 17:26:02 2003
From: asaraujo at if.sc.usp.br (Alexandre Suman de Araujo)
Date: Mon Aug  4 17:26:02 2003
Subject: [gmx-users] Mpi version of GROMACS - Doubt about its performance
In-Reply-To: <3F2E725D.2010208@nmr.chem.uu.nl>
References: <3F2E6EB2.8040707@if.sc.usp.br> <3F2E725D.2010208@nmr.chem.uu.nl>
Message-ID: <3F2E7DEC.5040302@if.sc.usp.br>

Shang-Te Danny Hsu wrote:

> Dear Alexandre,
>
> We also noticed the same problem with our SuSE8.1 Linux cluster with 
> mpich-1.2.1 and 1Gb/s ethernet interface. It only used less then 5% 
> CPU that was available when the parallel jobs were distributed 
> automatically. So far we found two temporary solutions:
>
> 1. Resubmit your parallel jobs repeatedly until it runs properly 
> (normally the third time it becomes okay)
>
> 2. Manually define the machines you'd like to distribute your jobs to.
>
> We are still testing other possibilities
>
> Cheers,
> Danny
>
> Alexandre Suman de Araujo wrote:
>
>> Hi GMXer
>>
>> I have a 4 nodes beowulf cluster and I installed de MPI version of 
>> GROMACS in it. To make a test I performed the same simulation in the 
>> 4 nodes and after in only one node.
>> The total time of simulation using the 4 nodes was only 10% faster 
>> than using only 1 node. This is correct???? Or somebody has a better 
>> performance?
>> The ethernet interface between the node is a 100Mb/s one... I think 
>> this is enough... or not???
>> Waiting coments.
>>
>> Best Regards.
>>
>
>
I'm using Red Hat 9.0 with LAM 7.0. . What do you mean with resubmit 
jobs??? Stop de mdrun(with a ctrl+c) e start it again??? Or another thing???
Thank's!

[]'s

-- 
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - Sa~o Carlos - Brasil




From spoel at xray.bmc.uu.se  Mon Aug  4 17:26:02 2003
From: spoel at xray.bmc.uu.se (David)
Date: Mon Aug  4 17:26:02 2003
Subject: [gmx-users] Calculation stopping
In-Reply-To: <002101c35a9b$e9b3a0c0$c47b14c8@HELIO>
References: <002101c35a9b$e9b3a0c0$c47b14c8@HELIO>
Message-ID: <1060011014.2700.0.camel@h28n2fls34o1123.telia.com>

On Mon, 2003-08-04 at 17:20, Tanos wrote:
>             Hi folks, 
> 
>             Lately I have faced a very strange problem when using
> GROMACS: My MD calculations stop without any apparent reason. I am
> trying 100 ps of MD in a system of 130.000 atoms, but when calculation
> reaches about step 25000, it suddenly stops without any error message.
> The files .job and .log remain unchanged as the calculation was yet
> on. Does someone has any idea of what can be happening ???????? 
2Gb files?

> 
>             Thanks in advance.
> 
>             Tanos C. C. Franca
> 
>             IME ? Rio de Janeiro - Brazil
> 
> 
> ---
> Outgoing mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
> Version: 6.0.504 / Virus Database: 302 - Release Date: 24/07/2003
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From ichorny at chemistry.maxwell.ucsf.edu  Mon Aug  4 18:00:02 2003
From: ichorny at chemistry.maxwell.ucsf.edu (Ilya Chorny)
Date: Mon Aug  4 18:00:02 2003
Subject: [gmx-users] RE: [gmx-users]
In-Reply-To: <67A9E751-C3AA-11D7-A210-000A95A099E0@stanford.edu>
Message-ID: <LIEFKEHIPPBDJLDIJKOIGEACCBAA.ichorny@chemistry.maxwell.ucsf.edu>

Is there a way to print forces during the simulation.
(Configurational free energy calculation)
Thanks Ilya






From hsu at panda.chem.uu.nl  Mon Aug  4 18:17:00 2003
From: hsu at panda.chem.uu.nl (Shang-Te Danny Hsu)
Date: Mon Aug  4 18:17:00 2003
Subject: [gmx-users] Mpi version of GROMACS - Doubt about its performance
References: <3F2E6EB2.8040707@if.sc.usp.br> <3F2E725D.2010208@nmr.chem.uu.nl> <3F2E7DEC.5040302@if.sc.usp.br>
Message-ID: <3F2E86EA.7060002@nmr.chem.uu.nl>

kill your job and start [mdrun_mpi] again

>> 1. Resubmit your parallel jobs repeatedly until it runs properly 
>> (normally the third time it becomes okay)
>>
> I'm using Red Hat 9.0 with LAM 7.0. . What do you mean with resubmit 
> jobs??? Stop de mdrun(with a ctrl+c) e start it again??? Or another 
> thing???
> Thank's!
> 
> []'s
> 


-- 
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl



From spoel at xray.bmc.uu.se  Mon Aug  4 18:51:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Mon Aug  4 18:51:01 2003
Subject: [gmx-users] RE: [gmx-users]
In-Reply-To: <LIEFKEHIPPBDJLDIJKOIGEACCBAA.ichorny@chemistry.maxwell.ucsf.edu>
References: 	 <LIEFKEHIPPBDJLDIJKOIGEACCBAA.ichorny@chemistry.maxwell.ucsf.edu>
Message-ID: <1060016084.2700.2.camel@h28n2fls34o1123.telia.com>

On Mon, 2003-08-04 at 17:59, Ilya Chorny wrote:
> Is there a way to print forces during the simulation.
> (Configurational free energy calculation)
nstfout = 1
> Thanks Ilya
> 
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From mashl at uiuc.edu  Mon Aug  4 18:56:01 2003
From: mashl at uiuc.edu (Jay Mashl)
Date: Mon Aug  4 18:56:01 2003
Subject: [gmx-users] Mpi version of GROMACS - Doubt about its performance
In-Reply-To: <3F2E6EB2.8040707@if.sc.usp.br>
Message-ID: <Pine.GSO.4.31.0308041150350.28708-100000@staff3.cso.uiuc.edu>

On Mon, 4 Aug 2003, Alexandre Suman de Araujo wrote:
> I have a 4 nodes beowulf cluster and I installed de MPI version of
> GROMACS in it. To make a test I performed the same simulation in the 4
> nodes and after in only one node.
> The  total time of simulation using the 4 nodes was only 10% faster than
> using only 1 node. This is correct???? Or somebody has a better performance?
> The ethernet interface between the node is a 100Mb/s one... I think this
> is enough... or not???
> Waiting coments.

Alexandre,

Maybe I am responding in the middle of a conversation, but in case not...

Scalability also depends on the number of atoms in your system as well as the
algorithms/parameters used to compute interactions.  Running a small system on
a lot of nodes will degrade performance because the nodes do not have enough
work to do in between communications.

Jay







From spoel at xray.bmc.uu.se  Mon Aug  4 19:03:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Mon Aug  4 19:03:00 2003
Subject: [gmx-users] Mpi version of GROMACS - Doubt about its
	performance
In-Reply-To: <Pine.GSO.4.31.0308041150350.28708-100000@staff3.cso.uiuc.edu>
References: <Pine.GSO.4.31.0308041150350.28708-100000@staff3.cso.uiuc.edu>
Message-ID: <1060016818.2699.4.camel@h28n2fls34o1123.telia.com>

On Mon, 2003-08-04 at 18:54, Jay Mashl wrote:
> On Mon, 4 Aug 2003, Alexandre Suman de Araujo wrote:
> > I have a 4 nodes beowulf cluster and I installed de MPI version of
> > GROMACS in it. To make a test I performed the same simulation in the 4
> > nodes and after in only one node.
> > The  total time of simulation using the 4 nodes was only 10% faster than
> > using only 1 node. This is correct???? Or somebody has a better performance?
> > The ethernet interface between the node is a 100Mb/s one... I think this
> > is enough... or not???
> > Waiting coments.
> 
> Alexandre,
> 
> Maybe I am responding in the middle of a conversation, but in case not...
> 
> Scalability also depends on the number of atoms in your system as well as the
> algorithms/parameters used to compute interactions.  Running a small system on
> a lot of nodes will degrade performance because the nodes do not have enough
> work to do in between communications.
This is correct. PME scales poorly. You could try the gromacs
benchmarks, in particular the DPPC one.
> 
> Jay
> 
> 
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From ygmu at theochem.uni-frankfurt.de  Tue Aug  5 09:40:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Tue Aug  5 09:40:01 2003
Subject: [gmx-users] linear molecule
In-Reply-To: <1059644932.27733.17.camel@werkman.bmc.uu.se>
Message-ID: <Pine.LNX.4.31.0308050937550.13197-100000@lisa.theochem.uni-frankfurt.de>

I have a linear molecule motif, like C=C=C=C,
Do you have some ideas to maintain such linear bonds ?

Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711




From spoel at xray.bmc.uu.se  Tue Aug  5 09:46:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Tue Aug  5 09:46:01 2003
Subject: [gmx-users] linear molecule
In-Reply-To: <Pine.LNX.4.31.0308050937550.13197-100000@lisa.theochem.uni-frankfurt.de>
References: 	 <Pine.LNX.4.31.0308050937550.13197-100000@lisa.theochem.uni-frankfurt.de>
Message-ID: <1060069778.3122.41.camel@h28n2fls34o1123.telia.com>

On Tue, 2003-08-05 at 09:39, Yuguang Mu wrote:
> I have a linear molecule motif, like C=C=C=C,
> Do you have some ideas to maintain such linear bonds ?
> 
Yes you have to use dummy particles for the atoms on the line.


> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From ygmu at theochem.uni-frankfurt.de  Tue Aug  5 10:02:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Tue Aug  5 10:02:01 2003
Subject: [gmx-users] linear molecule
In-Reply-To: <1060069778.3122.41.camel@h28n2fls34o1123.telia.com>
Message-ID: <Pine.LNX.4.31.0308050959390.13246-100000@lisa.theochem.uni-frankfurt.de>

The point is that , as to my knowledge, the dummy particles have no van
der Waals interaction. But I want to have these, How can I do ?

Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On 5 Aug 2003, David wrote:

> On Tue, 2003-08-05 at 09:39, Yuguang Mu wrote:
> > I have a linear molecule motif, like C=C=C=C,
> > Do you have some ideas to maintain such linear bonds ?
> >
> Yes you have to use dummy particles for the atoms on the line.



From spoel at xray.bmc.uu.se  Tue Aug  5 10:07:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Tue Aug  5 10:07:01 2003
Subject: [gmx-users] linear molecule
In-Reply-To: <Pine.LNX.4.31.0308050959390.13246-100000@lisa.theochem.uni-frankfurt.de>
References: 	 <Pine.LNX.4.31.0308050959390.13246-100000@lisa.theochem.uni-frankfurt.de>
Message-ID: <1060071056.3122.44.camel@h28n2fls34o1123.telia.com>

On Tue, 2003-08-05 at 10:01, Yuguang Mu wrote:
> The point is that , as to my knowledge, the dummy particles have no van
> der Waals interaction. But I want to have these, How can I do ?

yes they can.

see this example (from the gmxtest set)
[ defaults ]
;nonbond-type	combinationrule
1		1

; Division of mass over particles is not correct. Do not use
; for production.
[ atomtypes ]
;type	mass	charge	flavor	c6		c12
CMO	21.0	0.27	A	1.3827e-2	3.01e-5
NOO	20.0	-0.40	A	2.1475e-3	2.7734e-6
COO	0.0	0.13	D	2.5687e-3	3.968e-6

[ moleculetype ]
; name		nrexcl
SOL		1

[ atoms ]
;nr	type	resnr	residu	atom	cgnr	charge
1	CMO	1	SOL	Me1	1	0.27
2	NOO	1	SOL	N2	1	-0.40
3	COO	1	SOL	C3	1	0.13


[ constraints ]
;ai	aj	funct	dist
;1	2	1	0.146	1e6
;3	2	1	0.117	1e6
1	2	1	0.263	1e6

[ dummies2 ]
;
;calculating the position of the dummy atom
;
;  X1-----X3---X2
;
;  X3 = A1*X1 + A2*X2
;
;  A1 = 1 - dist(X1-X3)/dist(X1-X2) = 1 - 0.146/0.263 = 0.445
;  A2 = 1 - dist(X3-X2)/dist(X1-X2) = 1 - 0.117/0.263 = 0.555
; Dummy	from		funct	a	b
3	1	2       1	0.445	0.555

[ exclusions ]
1	2	3
2	1	3
3	1	2





-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From vdava at davapc1.bioch.dundee.ac.uk  Tue Aug  5 10:52:01 2003
From: vdava at davapc1.bioch.dundee.ac.uk (Daan van Aalten)
Date: Tue Aug  5 10:52:01 2003
Subject: [gmx-users] linear molecule
In-Reply-To: <Pine.LNX.4.31.0308050937550.13197-100000@lisa.theochem.uni-frankfurt.de>
Message-ID: <Pine.LNX.4.33.0308050941140.27973-100000@davapc1.bioch.dundee.ac.uk>

Dear Yuguang

The PRODRG server treats such linear systems correctly
(http://davapc1.bioch.dundee.ac.uk/prodrg)

cheers

Daan



On Tue, 5 Aug 2003, Yuguang Mu wrote:

> I have a linear molecule motif, like C=C=C=C,
> Do you have some ideas to maintain such linear bonds ?
>
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O



From nanyu101 at sina.com  Tue Aug  5 11:09:01 2003
From: nanyu101 at sina.com (nanyu101)
Date: Tue Aug  5 11:09:01 2003
Subject: [gmx-users] fail adding an external electric field
Message-ID: <20030805090828.26098.qmail@sina.com>

Dear gmx-users,
  I have tried to run MD with an external electric field for my system in the z direction:E_z = 1.0 0.5 0

  At the same time, I have run another MD without external electric fields. After 2ns MD running, I checked these two MD results, I found that energy terms,dipoles and RMSF are all the same, so I think I failed in adding external electric fields for my system. Would you please give me some advices?

Thanks a lot.

Best wishes,
nanyu
______________________________________
Best wishes,
Xianhui Wu
===================================================================
????9???????????????????????? (http://mail.sina.com.cn)


From spoel at xray.bmc.uu.se  Tue Aug  5 11:20:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Tue Aug  5 11:20:01 2003
Subject: [gmx-users] fail adding an external electric field
In-Reply-To: <20030805090828.26098.qmail@sina.com>
References: <20030805090828.26098.qmail@sina.com>
Message-ID: <1060075458.3124.46.camel@h28n2fls34o1123.telia.com>

On Tue, 2003-08-05 at 11:08, nanyu101 wrote:
> Dear gmx-users,
>   I have tried to run MD with an external electric field for my system in the z direction:E_z = 1.0 0.5 0
> 
>   At the same time, I have run another MD without external electric fields. After 2ns MD running, I checked these two MD results, I found that energy terms,dipoles and RMSF are all the same, so I think I failed in adding external electric fields for my system. Would you please give me some advices?
> 
http://www.gromacs.org/documentation/reference_3.1/online/mdp_opt.html#ef


> Thanks a lot.
> 
> Best wishes,
> nanyu
> ______________________________________
> Best wishes,
> Xianhui Wu
> ===================================================================
> ????9???????????????????????? (http://mail.sina.com.cn)
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From nanyu101 at sina.com  Tue Aug  5 11:29:01 2003
From: nanyu101 at sina.com (nanyu101)
Date: Tue Aug  5 11:29:01 2003
Subject: [gmx-users] fail adding an external electric field 2
Message-ID: <20030805092753.22033.qmail@sina.com>

Dear gmx-users,
  Thanks David's prompt reply. I have already read the manual and I think I have done as manual told,but I found my external electric field was not added.

 I want to add z direction 0.5V nm-1 like this:
E_z = 1.0  0.5  0.0

So would you please tell what 's wrong with me?

Thanks a lot

best wishes,
nanyu 
______________________________________
Best wishes,
Xianhui Wu
===================================================================
????9???????????????????????? (http://mail.sina.com.cn)


From spoel at xray.bmc.uu.se  Tue Aug  5 11:33:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Tue Aug  5 11:33:01 2003
Subject: [gmx-users] fail adding an external electric field 2
In-Reply-To: <20030805092753.22033.qmail@sina.com>
References: <20030805092753.22033.qmail@sina.com>
Message-ID: <1060076207.3126.48.camel@h28n2fls34o1123.telia.com>

On Tue, 2003-08-05 at 11:27, nanyu101 wrote:
> Dear gmx-users,
>   Thanks David's prompt reply. I have already read the manual and I think I have done as manual told,but I found my external electric field was not added.
> 
>  I want to add z direction 0.5V nm-1 like this:
> E_z = 1.0  0.5  0.0
how about
E_z = 1  0.5  0.0


> 
> So would you please tell what 's wrong with me?
> 
> Thanks a lot
> 
> best wishes,
> nanyu 
> ______________________________________
> Best wishes,
> Xianhui Wu
> ===================================================================
> ????9???????????????????????? (http://mail.sina.com.cn)
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From rboeckm at gwdg.de  Tue Aug  5 11:36:01 2003
From: rboeckm at gwdg.de (Rainer Boeckmann)
Date: Tue Aug  5 11:36:01 2003
Subject: [gmx-users] fail adding an external electric field 2
References: <20030805092753.22033.qmail@sina.com>
Message-ID: <3F2F7A5E.F3F11FEF@gwdg.de>

which gmx-version do you use? did you check the tpr-file? does the electric field appear in it (using gmxdump)?
cheers,
rainer

nanyu101 wrote:

> Dear gmx-users,
>   Thanks David's prompt reply. I have already read the manual and I think I have done as manual told,but I found my external electric field was not added.
>
>  I want to add z direction 0.5V nm-1 like this:
> E_z = 1.0  0.5  0.0
>
> So would you please tell what 's wrong with me?
>
> Thanks a lot
>
> best wishes,
> nanyu
> ______________________________________



From nanyu101 at sina.com  Tue Aug  5 11:54:01 2003
From: nanyu101 at sina.com (nanyu101)
Date: Tue Aug  5 11:54:01 2003
Subject: [gmx-users] fail adding an external electric field 3
Message-ID: <20030805095246.27134.qmail@sina.com>

Thanks for your prompt reply. My Gromacs version is 3.1.4.

I am checking my tpr-file with gmxdump now,I think it is in the tpr-file:
      efield-x:
         n = 0
      efield-xt:
         n = 0
      efield-y:
         n = 0
      efield-yt:
         n = 0
      efield-z:
         n = 1
           a = 0.000000e+00
           phi = 2.500000e+00
      efield-zt:
         n = 0


So what's the matter with my system?Thanks for your help.


Best wishes,
nanyu
______________________________________
Best wishes,
Xianhui Wu
===================================================================
????9???????????????????????? (http://mail.sina.com.cn)


From nanyu101 at sina.com  Tue Aug  5 11:56:01 2003
From: nanyu101 at sina.com (nanyu101)
Date: Tue Aug  5 11:56:01 2003
Subject: [gmx-users] E_z meanings
Message-ID: <20030805095511.23833.qmail@sina.com>

Dear gmx-users,
  
  E_z = 1.0 0.5 0

 I just do it as manual told. The first number is cosines, the sencond number 0.5 is electric fields. The third number is phase.

 Do you told me what's wrong with it?

Thanks a lot

best wishes,
nanyu 
______________________________________
Best wishes,
Xianhui Wu
===================================================================
????9???????????????????????? (http://mail.sina.com.cn)


From spoel at xray.bmc.uu.se  Tue Aug  5 12:02:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Tue Aug  5 12:02:00 2003
Subject: [gmx-users] fail adding an external electric field 3
In-Reply-To: <20030805095246.27134.qmail@sina.com>
References: <20030805095246.27134.qmail@sina.com>
Message-ID: <1060077928.3125.50.camel@h28n2fls34o1123.telia.com>

On Tue, 2003-08-05 at 11:52, nanyu101 wrote:
> Thanks for your prompt reply. My Gromacs version is 3.1.4.
> 
> I am checking my tpr-file with gmxdump now,I think it is in the tpr-file:
>       efield-x:
>          n = 0
>       efield-xt:
>          n = 0
>       efield-y:
>          n = 0
>       efield-yt:
>          n = 0
>       efield-z:
>          n = 1
>            a = 0.000000e+00
>            phi = 2.500000e+00

this tells you the amplitude is zero. The problem is that you specified
the number of cosines as a floating point number instead of as an
integer.

>       efield-zt:
>          n = 0
> 
> 
> So what's the matter with my system?Thanks for your help.
> 
> 
> Best wishes,
> nanyu
> ______________________________________
> Best wishes,
> Xianhui Wu
> ===================================================================
> ????9???????????????????????? (http://mail.sina.com.cn)
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From gk237 at cam.ac.uk  Tue Aug  5 17:08:01 2003
From: gk237 at cam.ac.uk (Giorgos Karvounis)
Date: Tue Aug  5 17:08:01 2003
Subject: [gmx-users] SPC - hydrogen bonding..
Message-ID: <3F2FC83A.ACF042EE@cam.ac.uk>

Dear all,

I am simulating a pentapeptide as a switterion in explicit SPC water. I
want to investigate the role of water during some folding events
(beta-turns) , especially when it comes down to water--> peptide
hydrogen bonding. We have implemented an algorithm for that, with
geometrical criteria, similar to GROMACS one.
The question is , i really see a "trend" of the water molecules  to be
hbonded to the peptide-NH's  (water oxygens) but there is no significant
OH2---O=C-peptide (except of the terminal COO-)...
I was really wondering if this could really be a normal situation , or
maybe an artifact due to SPC parameters...

Kind regards

George



From asaraujo at if.sc.usp.br  Tue Aug  5 20:17:01 2003
From: asaraujo at if.sc.usp.br (Alexandre Suman de Araujo)
Date: Tue Aug  5 20:17:01 2003
Subject: [gmx-users] Mpi version of GROMACS - Doubt about its	performance
In-Reply-To: <1060016818.2699.4.camel@h28n2fls34o1123.telia.com>
References: <Pine.GSO.4.31.0308041150350.28708-100000@staff3.cso.uiuc.edu> <1060016818.2699.4.camel@h28n2fls34o1123.telia.com>
Message-ID: <3F2FF7A1.5010802@if.sc.usp.br>

Hi GMXers

Thank's for everybody that help me. David was correct... the problem was 
with my system. I ran the simulation from benchmark and the difference 
was 50% between the single and parallel runnings.
Thanks for the help!

[]'s

-- 
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - S?o Carlos - Brasil




From jdejoan at emory.edu  Tue Aug  5 21:56:01 2003
From: jdejoan at emory.edu (Jason DeJoannis)
Date: Tue Aug  5 21:56:01 2003
Subject: [gmx-users] Clustermatic
Message-ID: <1060113314.3f300ba2d2182@webmail.service.emory.edu>

Dear All, 
 
 Does anyone have experience installing Clustermatic? 
If so did you encounter any hitches when using Gromacs? 
Our 9-node cluster currently uses Scyld Beowulf and  
Redhat 7. PME doesn't work in parallel. I have tested 
the bproc version of mpich that is installed and it works 
fine for the calculation of Pi.  
 
  I would like to install Redhat 8 with Clustermatic 3  
to make the system more up-to-date. Redhat 8 has the new  
glibc, which is important. Lots of things don't work with  
the older glibc - such as the recent edition of LAM which  
has bproc support. 
 
 From searching the mailing list it seems to me that there 
is very little mention of Beowulf/bproc clusters. Does 
that mean that most of you are using clusters with RSH  
and independent nodes? 
 
 -Jason 
 
--- 
Jason de Joannis, Ph.D. 
Chemistry Department, Emory University 
1515 Pierce Dr. NE, Atlanta, GA 30322 
Phone: (404) 712-2983 
Email: jdejoan at emory.edu 
http://userwww.service.emory.edu/~jdejoan 
 
 
 


From vraut at CLEMSON.EDU  Wed Aug  6 00:21:01 2003
From: vraut at CLEMSON.EDU (Vivek Raut)
Date: Wed Aug  6 00:21:01 2003
Subject: [gmx-users] how to introduce vacuum??
Message-ID: <5.1.1.5.2.20030805181433.00bc3208@mail.clemson.edu>

hi,

1: i have one water box with a protein & some other molecules. the height ( 
'c' in the dimensions of the system) of the box is 60 angstroms. Now I have 
to introduce vacuum in a section of the box ( say from height of 45 AU to 
55 AU)  how do i do that??

2: how to change permittivity in a part of system??

since by default we fill the box with water, the permittivity of the system 
is 80. i want to change it, how to do that??



*****************************************************************************************************************************************
Vivek Raut.
Graduate Research Assistant,
501 Rhodes Engineering Research Center
Clemson University, Clemson, SC 29634
Tel: 864-650-1431
Email: vraut at clemson.edu

*****************************************************************************************************************************************




From paloureiro at biof.ufrj.br  Wed Aug  6 01:06:01 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Wed Aug  6 01:06:01 2003
Subject: [gmx-users] how to introduce vacuum??
In-Reply-To: <5.1.1.5.2.20030805181433.00bc3208@mail.clemson.edu>
References: <5.1.1.5.2.20030805181433.00bc3208@mail.clemson.edu>
Message-ID: <1060124558.3f30378e647e3@webmail.biof.ufrj.br>

> hi,
> 
> 1: i have one water box with a protein & some other molecules. the height (
> 
> 'c' in the dimensions of the system) of the box is 60 angstroms. Now I have
> 
> to introduce vacuum in a section of the box ( say from height of 45 AU to 
> 55 AU)  how do i do that??
> 
If you want vacuum "above" the water layer then it`s easy: just enlarge the box
with editconf -f in.gro -o out.gro -box x y z-enlarged.
If you want a vacuum layer somwhere else, then I am afraid you will have to
write some simple program. For instance:
1)Cut your box "below" the coordinate you will want your vacuum layer to be with
editconf. Let`s assume you will change the z dimension.
2)Enlarge the z-dimension with editconf (vacuum). (prot.gro)
3)Create a water box with the same x y dimensions as above.(water.gro)
4)Change the coordinates of the water molecules so as they will be exactly above
the vacuum layer.
5)Merge the 2 files prot.gro and water.gro = vacuum .gro.
6)Don`t forget to edit the number of atoms line and the box dimensions line in
the vacuum.gro file.

Regards,

Pedro.
--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil 


From oliver at biop.ox.ac.uk  Wed Aug  6 02:40:01 2003
From: oliver at biop.ox.ac.uk (Oliver Beckstein)
Date: Wed Aug  6 02:40:01 2003
Subject: [gmx-users] how to introduce vacuum??
In-Reply-To: <1060124558.3f30378e647e3@webmail.biof.ufrj.br>
Message-ID: <Pine.LNX.4.21.0308060121180.860-102000@neuromancer.xibalba.org>

On Tue, 5 Aug 2003, Pedro Alexandre Lapido Loureiro wrote:

> > 1: i have one water box with a protein & some other molecules. the
> >height ( 'c' in the dimensions of the system) of the box is 60
> >angstroms. Now I have to introduce vacuum in a section of the box (
> >say from height of 45 AU to 55 AU) how do i do that??

You can use the killres.pl perl script that I attached; it allows you
to remove z-slices of given residues (typically SOL) from a gro
file. You will also need the Messages.pm perl module (also attached &
read the line USAGE in the comments). Run 'killres.pl --help' for,
well, help.

I put Messages.pm in ~/lib/perl and killres.pl somewhere in my PATH (eg
~/bin); then I'd try something like

killres.pl --output=with_vac.gro --resname=SOL --z1=4.5 --z2==5.5 \
           input.gro 

Note that this assumes that your waters are named as residues SOL and that
all distances in gro files are in nm (not Angstrom). It is important that
the first residue in the gro file starts with the number 1 (see bugs in
--help). 

I admit that this script is a bit too complicated (after all, a simple awk
would (almost) do the job, too) but it worked for me sofar *provided there
are less than 100,000 atoms* in your gro file---otherwise strange things
happen (any hints & feedback appreciated).

Oliver

-- 
Oliver Beckstein * oliver at bioch.ox.ac.uk
 http://indigo1.biop.ox.ac.uk/oliver/
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From nanyu101 at sina.com  Wed Aug  6 03:49:01 2003
From: nanyu101 at sina.com (nanyu101)
Date: Wed Aug  6 03:49:01 2003
Subject: [gmx-users] PME failed!!!!!
Message-ID: <20030806014739.29208.qmail@sina.com>

Dear gmx-users,
  I have failed trying to use PME for long-term coulomb 
potential with "Segmentation fault" in running mdrun, but if I
replaced the PME with cut-off, every is OK. Would you please tell me the reasons? Is my installation not completed?I have installed double precision.
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  cg/steep
emstep              =  0.001
emtol               =  1000
nsteps              =  200000
nscgsteep           =  100
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstlog              =  10
nstenergy           =  10
nstlist             =  10
pbc                 =  xyz
ns_type             =  grid
coulombtype         =  cut-off/pme
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9

Any comments are appreciated?
Thanks a lot.

Best wishes,
nanyu
______________________________________
Best wishes,
nanyu
===================================================================
????9???????????????????????? (http://mail.sina.com.cn)


From jllo at phy.ncu.edu.tw  Wed Aug  6 08:00:01 2003
From: jllo at phy.ncu.edu.tw (Jia-Lin Lo)
Date: Wed Aug  6 08:00:01 2003
Subject: [gmx-users] Where is the Drug-enzyme tutorial ?
Message-ID: <000a01c35be0$1762f8f0$341e738c@folding>

Dear gmx users;
     I have seen many people are working on drug-
enzyme tutorial. Is there any people can tell me
where can I find this tutorial? Thank you very 
much

Jialin
==============================================================
Jia-lin Lo
Dept. of Physics ,National Central University,
Chung Li , Taiwan,
e-mail : jllo at phy.ncu.edu.tw  Home page: http://pooh.phy.ncu.edu.tw/~jllo/
==============================================================
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From Xavier.Periole at physbio.mssm.edu  Wed Aug  6 08:49:01 2003
From: Xavier.Periole at physbio.mssm.edu (Xavier Periole)
Date: Wed Aug  6 08:49:01 2003
Subject: [gmx-users] PME failed!!!!!
In-Reply-To: <20030806014739.29208.qmail@sina.com>
Message-ID: <B05621CC-C796-11D7-B15F-0050E41E2965@physbio.mssm.edu>


Try to increase your cutoff to 1.2 nm should do it !
If not ...

XAvier



From malcolm.b.gillies at anu.edu.au  Wed Aug  6 09:01:01 2003
From: malcolm.b.gillies at anu.edu.au (Malcolm Gillies)
Date: Wed Aug  6 09:01:01 2003
Subject: [gmx-users] OPLS-AA Coulomb-14 energies incorrect?
Message-ID: <1060153193.22019.241.camel@bakunin>

Hi,

I appear to have found an error in the calculation of the Coulomb 1-4
energies using the GROMACS OPLS-AA implementation. Have potential
energies calculated with this force field been validated against those
from some other implementation (e.g. BOSS, MCPRO, Impact, MacroModel
etc)?

The Coulomb (SR) component of the GROMACS energy agrees with the
corresponding energy from TINKER (i.e. as calculated by setting
chg-14-scale to 0.0), but the Coulomb-14 energy is out by a sizeable
percentage. i.e for the attached file GROMACS reports 224.739 kJ/mol
while TINKER reports 258.3687 kJ/mol.

I've attached copies of my GROMACS and TINKER input files. I had to
modify the TINKER 4.0 oplsaa.prm file to include an atom type for the
GLY zwitterion CA with the correct charge; I've included this
modification as a patch file. 

Comparing GROMACS (OPLS-AA parameter files checked out of CVS about
a month ago) and TINKER 4.0 (with the supplied oplsaa.prm parameters) on
a couple of potential energy calculations, I found that they agree on
the bond stretch, bend and LJ energies. The improper dihedral energies
differ, though this may be due to a problem with TINKER. GROMACS uses
some updated proper dihedral parameters, absent from the TINKER
oplsaa.prm file, so for most structures the proper dihedral energies are
not comparable (though they seem to match for the glycine zwitterion).

cheers,

Malcolm
--
Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
John Curtin School of Medical Research, Australian National University

-------------- next part --------------
;
;	File 'GLY.top' was generated
;	By user: mxg (252)
;	On host: bakunin
;	At date: Wed Aug  6 15:11:56 2003
;
;	This is your topology file
;	"That Was Really Cool" (Butthead)
;
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Protein_A           3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1   opls_287      1    GLY      N      1       -0.3    14.0067   ; qtot -0.3
     2   opls_290      1    GLY     H1      1       0.33      1.008   ; qtot 0.03
     3   opls_290      1    GLY     H2      1       0.33      1.008   ; qtot 0.36
     4   opls_290      1    GLY     H3      1       0.33      1.008   ; qtot 0.69
     5   opls_298      1    GLY     CA      1       0.09     12.011   ; qtot 0.78
     6   opls_140      1    GLY    HA1      1       0.06      1.008   ; qtot 0.84
     7   opls_140      1    GLY    HA2      1       0.06      1.008   ; qtot 0.9
     8   opls_271      1    GLY      C      2        0.7     12.011   ; qtot 1.6
     9   opls_272      1    GLY     O1      2       -0.8    15.9994   ; qtot 0.8
    10   opls_272      1    GLY     O2      2       -0.8    15.9994   ; qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1 
    1     3     1 
    1     4     1 
    1     5     1 
    5     6     1 
    5     7     1 
    5     8     1 
    8     9     1 
    8    10     1 

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     9     1 
    1    10     1 
    2     8     1 
    3     8     1 
    4     8     1 
    6     9     1 
    6    10     1 
    7     9     1 
    7    10     1 

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1     3     1 
    2     1     4     1 
    2     1     5     1 
    3     1     4     1 
    3     1     5     1 
    4     1     5     1 
    1     5     6     1 
    1     5     7     1 
    1     5     8     1 
    6     5     7     1 
    6     5     8     1 
    7     5     8     1 
    5     8     9     1 
    5     8    10     1 
    9     8    10     1 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
    2     1     5     6     3 
    2     1     5     7     3 
    2     1     5     8     3 
    3     1     5     6     3 
    3     1     5     7     3 
    3     1     5     8     3 
    4     1     5     6     3 
    4     1     5     7     3 
    4     1     5     8     3 
    1     5     8     9     3 
    1     5     8    10     3 
    6     5     8     9     3 
    6     5     8    10     3 
    7     5     8     9     3 
    7     5     8    10     3 

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3
    5    10     9     8     1    improper_O_C_X_Y

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Protein_A           1
-------------- next part --------------
S  C  A  M  O  R  G
   10
    1GLY      N    1   0.442   0.702  -0.555
    1GLY     H1    2   0.470   0.621  -0.607
    1GLY     H2    3   0.456   0.685  -0.457
    1GLY     H3    4   0.345   0.721  -0.572
    1GLY     CA    5   0.522   0.816  -0.596
    1GLY    HA1    6   0.628   0.792  -0.578
    1GLY    HA2    7   0.509   0.832  -0.704
    1GLY      C    8   0.490   0.946  -0.524
    1GLY     O1    9   0.391   0.942  -0.430
    1GLY     O2   10   0.563   1.056  -0.559
   0.28265   0.43423   0.27368
-------------- next part --------------
title               =  molecular dynamics
cpp                 =  /lib/cpp
constraints         =  none
integrator          =  md
dt                  =  0.001    ; ps !
nsteps              =  1
comm_mode           =  none
nstcomm             =  0
nstxout             =  1
nstvout             =  10000
nstfout             =  0
pbc                 =  no
nstlist             =  0
ns_type             =  simple
rlist               =  0.0
rcoulomb            =  0.0
rvdw                =  0.0
;coulombtype         =  cutoff
;rcoulomb_switch     =  0.0
dispcorr            =  no
;epsilon_surface     =  78.0
;fourierspacing      =  0.1
;pmeorder            =  6
;loptimizefft         =  no
; Nose-Hoover coupling is on in two groups
Tcoupl              =  no
;tau_t               =  0.1      0.1
;tc-grps             =  protein  sol
;ref_t               =  300      300
; Pressure coupling is on
Pcoupl              =  no
;Pcoupltype          =  isotropic
;tau_p               =  0.5
;compressibility     =  4.5e-5
;ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
-------------- next part --------------
    10
     1  N3     4.420000    7.020000   -5.550000   146     2     5     6     7
     2  CT     5.220000    8.160000   -5.960000   211     1     3     8     9
     3  C_3    4.900000    9.460000   -5.240000   111     2     4    10
     4  O2     3.91        9.42       -4.30       112     3
     5  H3     4.70        6.21       -6.07       151     1
     6  H3     4.56        6.85       -4.57       151     1
     7  H3     3.45        7.21       -5.72       151     1
     8  HC     6.280000    7.920000   -5.780000     6     2
     9  HC     5.090000    8.320000   -7.040000     6     2
    10  O2     5.63       10.56       -5.59       112     3
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From lindahl at stanford.edu  Wed Aug  6 09:26:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Wed Aug  6 09:26:01 2003
Subject: [gmx-users] OPLS-AA Coulomb-14 energies incorrect?
In-Reply-To: <1060153193.22019.241.camel@bakunin>
Message-ID: <EE5C7E4F-C7DE-11D7-B745-000A95A099E0@stanford.edu>

Hi Malcolm,

It's always nice to see comparisons!

First - I think I know what the cause of the difference might be. By 
default, the pdb2gmx program does not generate 1,4 interactions for 
hydrogens since that's the prescribed setup for the other force fields. 
  Use the -H14 flag for pdb2gmx to get the OPLS-AA standard.

This will probably be the default in future Gromacs versions (it's 
already changed in CVS), but we would probably confuse users more by 
changing the default in a point release....

The parameters have mainly been cross-validated with Tinker, the 
energies for aminoacids in the Jorgensen publications (check the header 
of the force field for references) and MacroModel.

> The Coulomb (SR) component of the GROMACS energy agrees with the
> corresponding energy from TINKER (i.e. as calculated by setting
> chg-14-scale to 0.0), but the Coulomb-14 energy is out by a sizeable
> percentage. i.e for the attached file GROMACS reports 224.739 kJ/mol
> while TINKER reports 258.3687 kJ/mol.

Again, I would guess that difference is due to not using the -H14 flag. 
You are right that the relative difference for this term is large, but 
compared to the total nonbonded energy it is very small, so it is not 
likely to have affected your simulations significantly.

> Comparing GROMACS (OPLS-AA parameter files checked out of CVS about
> a month ago) and TINKER 4.0 (with the supplied oplsaa.prm parameters) 
> on
> a couple of potential energy calculations, I found that they agree on
> the bond stretch, bend and LJ energies. The improper dihedral energies
> differ, though this may be due to a problem with TINKER. GROMACS uses
> some updated proper dihedral parameters, absent from the TINKER.

Right - the bonded parameters are essentially the Amber ones, and they 
haven't been changed in years. There are two major modifications to the 
OPLS torsion angles not present in Tinker (one by Jorgensen in 1999 and 
another set that formed the OPLS-AA/L version in 2001). I also recall 
there were some minor issues in Tinker; some uncommon charge groups 
would not end up being neutral with their charges.

Another issue you might stumble upon is that Amber and Gromacs used 
different atom orders for the improper dihedrals. I've changed this in 
our later versions, but this is not significant. The difference is only 
second order, and the improper force constants are just 
order-of-magnitude guesses anyway.  I've just uploaded a tarball with 
the latest OPLS parameters to the contrib section of www.gromacs.org if 
you want to play with it.

In all cases of doubt I've used the "original" values, i.e. Amber for 
bonded interactions and Jorgensen/Kaminski for torsions and charges. I 
also communicated rather extensively with Bill Jorgensen and Julian 
Tirado-Rives during the implementation (they were quite helpful).

Thanks for the help with checking things - and let me know if the 
problems persist with -H14.

Cheers,

Erik



From feenstra at chem.vu.nl  Wed Aug  6 09:47:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Wed Aug  6 09:47:01 2003
Subject: [gmx-users] Re: Inquiry Again.
In-Reply-To: <20030801214131.762.qmail@web21512.mail.yahoo.com>
References: <20030801214131.762.qmail@web21512.mail.yahoo.com>
Message-ID: <3F2E8B13.2010002@chem.vu.nl>

Albert Sun wrote:
> Dear Anton and Gmx-users,
>  
> If without bonds, I think the top file (as shown in urea.top - manual page 100) will like this:

First off, but I'm not 100% sure, the .top starts with an obligatory
[defaults] section, indicating things like exclusions along bonds (not
relevant for you) and LJ combination rules. Check the manual.

> [moleculetype] ... [atom] ... [bonds]  ; no need to input

Looks good up to here, but I don't see where you need [pairs]. These are
normally used as a modification to a dihedral potential, i.e. the LJ
interaction for the 1-4 pair on a dihedral angle should often be less
than the normal LJ interaction.

> [pairs]
> ;ai       aj        funct           b0       kb
[...]
> [angles]  ;  no need to input ... [dihedrals];  no need to input 

Looks good again, but for position restraint one usually wants a switch
to turn them on or off, so you in stead of:

> [position_restraints}
> 1    1    1000     1000    10000
> ...

You would put:
#ifdef POSRES
[position_restraints]
1    1    1000   1000   1000
...
#endif

using a switch in your .mdp file like 'defines = -DPOSRES'

> ... #include  "spc.itp" ... [system] ... [molecules] ...

Looks good again.

> Besides, how could we select ' without bonds'  when we do pdb2gmx or by modifying 
> .pdb file ?

No, no! pdb2gmx is for *building* *topologies*, mainly for biopolymers
like proteins or DNA. If you build your own topology, or use one from
e.g. ProDrg, you *do* *not* *need* pdb2gmx! My apologies if I seem too
explicit here, but I see many people using pdb2gmx when it is not
necessary, which often causes all kinds of terrible problems, not to
mention a lot of unnecessary work!

So, if you build your topology (= .top file), you will not have any
bonds. You should use your .gro (or .pdb) file with coordinates and
.top file with topology directly as input to grompp (and an .mdp file
of course). No bonds in your .top file = no bonds in your .tpr file!

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Wed Aug  6 09:47:02 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Wed Aug  6 09:47:02 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <1059993009.12989.25.camel@h28n2fls34o1123.telia.com>
References: <DB290E8C-C661-11D7-B092-000393BB411E@weizmann.ac.il> <1059993009.12989.25.camel@h28n2fls34o1123.telia.com>
Message-ID: <3F2E8B4D.20502@chem.vu.nl>

David wrote:
> I think that option has been lost a long while ago...

Yes - it was found to be completely dysfunctional.
Sorry we forgot to update the manual.... ;-{


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From bgroot at gwdg.de  Wed Aug  6 09:50:01 2003
From: bgroot at gwdg.de (Bert de Groot)
Date: Wed Aug  6 09:50:01 2003
Subject: [gmx-users] how to introduce vacuum??
References: <Pine.LNX.4.21.0308060121180.860-102000@neuromancer.xibalba.org>
Message-ID: <3F30B2F8.4FB76DC0@gwdg.de>

Oliver Beckstein wrote:
> 
> On Tue, 5 Aug 2003, Pedro Alexandre Lapido Loureiro wrote:
> 
> > > 1: i have one water box with a protein & some other molecules. the
> > >height ( 'c' in the dimensions of the system) of the box is 60
> > >angstroms. Now I have to introduce vacuum in a section of the box (
> > >say from height of 45 AU to 55 AU) how do i do that??
> 

[..]

> I admit that this script is a bit too complicated (after all, a simple awk
> would (almost) do the job, too) but it worked for me sofar *provided there
> are less than 100,000 atoms* in your gro file---otherwise strange things
> happen (any hints & feedback appreciated).
> 


this small awk might do the job too (on a pdb file):

($3 != "HW1" && $3 != "HW2") {keep[$5]=1}
($3 == "OW" && ($8 > 45 && $8 < 55)) {keep[$5]=0}
keep[$5]==1 {print $0}


(provided that the pdb does *not* contain chain identifiers, otherwise
the $8 should be a $9 and the $5 a $6).

--

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________


From malcolm.b.gillies at anu.edu.au  Wed Aug  6 09:57:01 2003
From: malcolm.b.gillies at anu.edu.au (Malcolm Gillies)
Date: Wed Aug  6 09:57:01 2003
Subject: [gmx-users] OPLS-AA Coulomb-14 energies incorrect?
In-Reply-To: <EE5C7E4F-C7DE-11D7-B745-000A95A099E0@stanford.edu>
References: <EE5C7E4F-C7DE-11D7-B745-000A95A099E0@stanford.edu>
Message-ID: <1060156553.22019.287.camel@bakunin>

On Wed, 2003-08-06 at 17:23, Erik Lindahl wrote:
> First - I think I know what the cause of the difference might be. By 
> default, the pdb2gmx program does not generate 1,4 interactions for 
> hydrogens since that's the prescribed setup for the other force fields. 
>   Use the -H14 flag for pdb2gmx to get the OPLS-AA standard.

Thanks, with the -H14 flag, the Coulomb energies now agree to within a
fraction of a percent.

> This will probably be the default in future Gromacs versions (it's 
> already changed in CVS), but we would probably confuse users more by 
> changing the default in a point release....

Right, perhaps a warning in the header of the ffoplsaa.itp file might be
in order, if it's not a default for pdb2gmx.

> I've just uploaded a tarball with 
> the latest OPLS parameters to the contrib section of www.gromacs.org if 
> you want to play with it.

Great, thanks!

cheers,

Malcolm
--
Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
John Curtin School of Medical Research, Australian National University




From kay.gottschalk at weizmann.ac.il  Wed Aug  6 09:58:01 2003
From: kay.gottschalk at weizmann.ac.il (Kay Gottschalk)
Date: Wed Aug  6 09:58:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <3F2E8B4D.20502@chem.vu.nl>
Message-ID: <A1D6F7EE-C7E3-11D7-86EE-000393BB411E@weizmann.ac.il>

No problem with manual:) I'd just like to know how people do the rdf 
for single surface atoms. There must be some correction for the protein 
volume (which excludes water of course) in the sphere-section for which 
the density function is calculated. Is there a clever way to do that in 
Gromacs? Actually, I am not sure I am making myself clear here... At 
any rate, suggestions would be highly appreciated.
Cheers,
Kay.

> David wrote:
>> I think that option has been lost a long while ago...
>
> Yes - it was found to be completely dysfunctional.
> Sorry we forgot to update the manual.... ;-{
>
>
> -- 
> Groetjes,
>
> Anton
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> |             | "If You See Me Getting High, Knock Me Down"           |
> |             | (Red Hot Chili Peppers)                               |
> |_____________|_______________________________________________________|
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
>
>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel



From spoel at xray.bmc.uu.se  Wed Aug  6 09:59:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Wed Aug  6 09:59:01 2003
Subject: [gmx-users] OPLS-AA Coulomb-14 energies incorrect!
In-Reply-To: <1060153193.22019.241.camel@bakunin>
References: <1060153193.22019.241.camel@bakunin>
Message-ID: <1060156973.1743.9.camel@h28n2fls34o1123.telia.com>

On Wed, 2003-08-06 at 08:59, Malcolm Gillies wrote:
> Hi,
> 
> I appear to have found an error in the calculation of the Coulomb 1-4
> energies using the GROMACS OPLS-AA implementation. Have potential
> energies calculated with this force field been validated against those
> from some other implementation (e.g. BOSS, MCPRO, Impact, MacroModel
> etc)?
> 
> The Coulomb (SR) component of the GROMACS energy agrees with the
> corresponding energy from TINKER (i.e. as calculated by setting
> chg-14-scale to 0.0), but the Coulomb-14 energy is out by a sizeable
> percentage. i.e for the attached file GROMACS reports 224.739 kJ/mol
> while TINKER reports 258.3687 kJ/mol.
I've found the source of the error: the interactions between the
N-terminal hydrogens and the HA* are not listed in the pair interaction
list. When you do so the energies are identical. (see atached modified
gro file and test.pl script).

I've checked for another OPLS topology that I had lying around and found
- for the N-terminus it is incorrect there as well
- in general 14 interactions between H's are turned off (they are
treated as normal interactions).

However pdb2gmx has a flag -H14 which turns on 1-4 interactions between
H atoms. It seems therefore that OPLS calculations need to be performed
with this option:

pdb2gmx -H14 [ more flags ]

(in a single test on a pdb file I find that the HH 1-4 interactions are
indeed listed when the flag is used)

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- next part --------------
S  C  A  M  O  R  G
   10
    1GLY      N    1   0.442   0.702  -0.555    -0.3 
    1GLY     H1    2   0.470   0.621  -0.607    0.33 
    1GLY     H2    3   0.456   0.685  -0.457    0.33 
    1GLY     H3    4   0.345   0.721  -0.572    0.33 
    1GLY     CA    5   0.522   0.816  -0.596    0.09 
    1GLY    HA1    6   0.628   0.792  -0.578    0.06 
    1GLY    HA2    7   0.509   0.832  -0.704    0.06 
    1GLY      C    8   0.490   0.946  -0.524     0.7 
    1GLY     O1    9   0.391   0.942  -0.430    -0.8 
    1GLY     O2   10   0.563   1.056  -0.559    -0.8 
   0.28265   0.43423   0.27368
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From spoel at xray.bmc.uu.se  Wed Aug  6 10:04:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Wed Aug  6 10:04:01 2003
Subject: [gmx-users] PME failed!!!!!
In-Reply-To: <20030806014739.29208.qmail@sina.com>
References: <20030806014739.29208.qmail@sina.com>
Message-ID: <1060157264.1743.11.camel@h28n2fls34o1123.telia.com>

On Wed, 2003-08-06 at 03:47, nanyu101 wrote:
> Dear gmx-users,
>   I have failed trying to use PME for long-term coulomb 
> potential with "Segmentation fault" in running mdrun, but if I
> replaced the PME with cut-off, every is OK. Would you please tell me the reasons? Is my installation not completed?I have installed double precision.
> define              =  -DFLEX_SPC

you have to give more details. Is your FFTW compiled in double precision
too? Do you have the same problem in MD (instead of CG) etc.    

> constraints         =  none
> integrator          =  cg/steep
> emstep              =  0.001
> emtol               =  1000
> nsteps              =  200000
> nscgsteep           =  100
> nstcomm             =  1
> nstxout             =  50
> nstvout             =  1000
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> pbc                 =  xyz
> ns_type             =  grid
> coulombtype         =  cut-off/pme
> rlist               =  0.9
> rcoulomb            =  0.9
> rvdw                =  0.9
> 
> Any comments are appreciated?
> Thanks a lot.
> 
> Best wishes,
> nanyu
> ______________________________________
> Best wishes,
> nanyu
> ===================================================================
> ????9???????????????????????? (http://mail.sina.com.cn)
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From nanyu101 at sina.com  Wed Aug  6 12:26:02 2003
From: nanyu101 at sina.com (nanyu101)
Date: Wed Aug  6 12:26:02 2003
Subject: [gmx-users] PME failed!!!!! again
Message-ID: <20030806083033.29942.qmail@sina.com>

Dear gmx-users,
  Thanks for David and Xavier Periole 's prompt reply.

Firstly, I have tried to use cutoff 1.2 just as Xavier Periole told, but the same problem happened with " 15848 Segmentation fault".

Secondly, I have just installation my FFTW with double precision.And I didn't find that Gromacs should be installed with double precision in installation web.

I have run with pme model in MD after with cut-off in minimization, the same problem happened with " 15899 Segmentation fault".

 Thanks for your kind assistant.

Best wishes,
Xianhui Wu
______________________________________
Best wishes,
nanyu
===================================================================
????9???????????????????????? (http://mail.sina.com.cn)


From DaJustice1 at aol.com  Wed Aug  6 14:23:01 2003
From: DaJustice1 at aol.com (DaJustice1 at aol.com)
Date: Wed Aug  6 14:23:01 2003
Subject: [gmx-users] Amber OPLS dihedral conversion to GROMACS RB
Message-ID: <121.24ae73df.2c624cdf@aol.com>

Dear GMX Users,
 
I am attempting to convert Amber OPLS dihedral parameters to GMX RB 
parameters, but I?m having some trouble.   I have searched through the archives and 
found replies about the same problem.   The replies state that the conversion is 
described in the GMX Users manual.   I have read the force field section 
covering dihedral conversion to RB, but I still am not sure how to proceed.   Amber 
OPLS has multiple definitions for dihedrals using different PN, but GMX only 
has one line containing the six RB parameters C 0-5.   If someone in the list 
has experience with these conversions, please enlighten me.

Thank you,

David Justice
Researcher
Gogonea Computational Chem. Group    
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From vcb25 at cam.ac.uk  Wed Aug  6 17:39:00 2003
From: vcb25 at cam.ac.uk (Vincent Ballenegger)
Date: Wed Aug  6 17:39:00 2003
Subject: [gmx-users] g_msd, segmentation fault with options -trestart and -mol
Message-ID: <3F3120CF.3030803@cam.ac.uk>

Hi there,

Several people mentioned already in this mailing list that g_msd 
generates a segmentation fault when the options -trestart and -mol are 
used together. Has anyone figured out what causes this error?

Vincent



From malcolm.b.gillies at anu.edu.au  Thu Aug  7 04:54:01 2003
From: malcolm.b.gillies at anu.edu.au (Malcolm Gillies)
Date: Thu Aug  7 04:54:01 2003
Subject: [gmx-users] Amber OPLS dihedral conversion to GROMACS RB
In-Reply-To: <121.24ae73df.2c624cdf@aol.com>
References: <121.24ae73df.2c624cdf@aol.com>
Message-ID: <1060224761.29524.32.camel@bakunin>

Hi David,

The conversion formula you need is on page 62 of the GROMACS manual
(equation 4.54). Assuming the phase angles for PN= 1, 2 and 3 are 0,
180, and 0 degrees, respectively, then Vn in equation 4.54 is equal to
PK / IDIVF for the line where PN=n

e.g.

    X -C -CA-X    4   14.50        180.0             2.         

gives a V2 = 14.5 / 4 = 3.625 kcal/mol

For a particular dihedral, you need to accumulate all the Vn terms from
different lines of the AMBER parameter file and then convert them into a
single set of RB parameters.

See also

    http://amber.scripps.edu/doc6/html/AMBER-sh-19.3.html

under "Dihedral parameters" for the AMBER torsional energy function.

cheers,

Malcolm
--
Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
John Curtin School of Medical Research, Australian National University

On Wed, 2003-08-06 at 22:21, DaJustice1 at aol.com wrote:
> Dear GMX Users,
> 
> I am attempting to convert Amber OPLS dihedral parameters to GMX RB
> parameters, but I?m having some trouble.  I have searched through the
> archives and found replies about the same problem.  The replies state
> that the conversion is described in the GMX Users manual.  I have read
> the force field section covering dihedral conversion to RB, but I
> still am not sure how to proceed.  Amber OPLS has multiple definitions
> for dihedrals using different PN, but GMX only has one line containing
> the six RB parameters C 0-5.  If someone in the list has experience
> with these conversions, please enlighten me.
> 
> Thank you,
> 
> David Justice
> Researcher
> Gogonea Computational Chem. Group   




From feenstra at chem.vu.nl  Thu Aug  7 09:15:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug  7 09:15:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <A1D6F7EE-C7E3-11D7-86EE-000393BB411E@weizmann.ac.il>
References: <A1D6F7EE-C7E3-11D7-86EE-000393BB411E@weizmann.ac.il>
Message-ID: <3F312782.6080207@chem.vu.nl>

Kay Gottschalk wrote:
> No problem with manual:) I'd just like to know how people do the rdf for 
> single surface atoms. There must be some correction for the protein 
> volume (which excludes water of course) in the sphere-section for which 
> the density function is calculated. Is there a clever way to do that in 
> Gromacs? Actually, I am not sure I am making myself clear here... At any 
> rate, suggestions would be highly appreciated.

You'll have to do some explaining here ;-(

We've used rdf's (in the past) for comparison with e.g. neutron scattering
for e.g. water. The angle dependence was added to analyze coordination
shell structure in liquid water. So, no surfaces there, and no protein.

What do you mean by 'single surface atom', and what correction for protein
volume should there be? It may be that g_sas has an option to calculate
the protein surface as well as the volume, but it has been upgraded since
I last used it so I'm not sure.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Thu Aug  7 09:15:02 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug  7 09:15:02 2003
Subject: [gmx-users] Drug - Enzyme tutorial
In-Reply-To: <003201c3599a$a80a2a60$6480a8c0@dasmalchi>
References: <003201c3599a$a80a2a60$6480a8c0@dasmalchi>
Message-ID: <3F312924.7060801@chem.vu.nl>

Dastmalchi wrote:
> Dear Collegues,
> 
> I am new to GROMACS, and was going through the Drug-Enzyme tutorial. I am using
> CROMACS on a PC running WinXP. When I issue the following command
> "genbox -cp trp.gro -cs spc216.gro -o trp_b4em.gro -p trp.top", I get an empty
> trp.top file. I tried to edit the top file using temp.top and did many other
> thing to continue the tutorial but it didn't work. I was wondering if you could
> kindly help me out with this.

Hmm. This probably is a bug (and if so, it's my fault) ;-(

The workaround is simple: do not put the '-p trp.top' on the commandline,
and edit the .top file yourself: it is very easy: Genbox tells
you when if finishes how many waters it has added. Just add a line at the
end of the .top file for that number of water molecules, so the end of your
file would look something like this:
....
[ system ]
protein in water

[ molecules ]
Protein		1
Drug		1
SOL		4125

(your mileage may vary)

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Thu Aug  7 09:15:04 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug  7 09:15:04 2003
Subject: [gmx-users] cpp and SGI irix 6.5
In-Reply-To: <1059994861.12989.28.camel@h28n2fls34o1123.telia.com>
References: <E19jcfD-0000tE-00@www.bham.ac.uk> <1059994861.12989.28.camel@h28n2fls34o1123.telia.com>
Message-ID: <3F3129CB.1080105@chem.vu.nl>

David wrote:
> On Mon, 2003-08-04 at 12:34, jxs818 at bham.ac.uk wrote:
> 
>>Hi All, 
>>I have compiled gromacs on an SGI irix 6.5, but there is no 
>>CPP on the system. Where can i download a copy (GPL).
> 
> 
> You can find something called freeware on the SGI website. That has
> amongst other the gcc compiler. You could check whether it is not yet
> installed in your system, default directory would be /usr/freeware

No, no! It is not possible. Without cpp you cannot compile!
So, if you have compiled gromacs, cpp must be somewhere on your system,
e.g. /usr/local/lib/cpp, or /usr/local/bin/cpp. If all else fails, you
could try 'find / -name cpp' to search all your harddisks for 'cpp'.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Thu Aug  7 09:15:05 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug  7 09:15:05 2003
Subject: [gmx-users] fail adding an external electric field 2
In-Reply-To: <3F2F7A5E.F3F11FEF@gwdg.de>
References: <20030805092753.22033.qmail@sina.com> <3F2F7A5E.F3F11FEF@gwdg.de>
Message-ID: <3F312B39.10902@chem.vu.nl>

Rainer Boeckmann wrote:
> which gmx-version do you use? did you check the tpr-file? does the electric
> field appear in it (using gmxdump)?

Or, easier, 'gmxcheck -s1 <without_ef>.tpr -s2 <with_ef>.tpr' will print
all differences between the .tpr files.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Thu Aug  7 09:15:06 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug  7 09:15:06 2003
Subject: [gmx-users] E_z meanings
In-Reply-To: <20030805095511.23833.qmail@sina.com>
References: <20030805095511.23833.qmail@sina.com>
Message-ID: <3F312BBB.2050103@chem.vu.nl>

nanyu101 wrote:
> Dear gmx-users,
>   
>   E_z = 1.0 0.5 0
> 
>  I just do it as manual told. The first number is cosines, the sencond number 0.5 is electric fields. The third number is phase.

As David suggested, try with the first number as '1' in stead of '1.0'.

If this really fixes your problem, I would say it is a bug and should be
fixed. Our input syntax should not be so strict!


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Thu Aug  7 09:15:07 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug  7 09:15:07 2003
Subject: [gmx-users] how to introduce vacuum??
In-Reply-To: <Pine.LNX.4.21.0308060121180.860-102000@neuromancer.xibalba.org>
References: <Pine.LNX.4.21.0308060121180.860-102000@neuromancer.xibalba.org>
Message-ID: <3F312C5E.7050105@chem.vu.nl>

Oliver Beckstein wrote:
> Note that this assumes that your waters are named as residues SOL and that
> all distances in gro files are in nm (not Angstrom). It is important that
> the first residue in the gro file starts with the number 1 (see bugs in
> --help). 

Just a note: the .gro file format explicitly requires nanometers. Angstroms
should *not* be used.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Thu Aug  7 09:15:08 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug  7 09:15:08 2003
Subject: [gmx-users] Amber OPLS dihedral conversion to GROMACS RB
In-Reply-To: <121.24ae73df.2c624cdf@aol.com>
References: <121.24ae73df.2c624cdf@aol.com>
Message-ID: <3F312ECB.70908@chem.vu.nl>

DaJustice1 at aol.com wrote:
> Dear GMX Users,
>  
> I am attempting to convert Amber OPLS dihedral parameters to GMX RB 
> parameters, but I?m having some trouble.   I have searched through the archives and 
> found replies about the same problem.   The replies state that the conversion is 
> described in the GMX Users manual.   I have read the force field section 
> covering dihedral conversion to RB, but I still am not sure how to proceed.   Amber 
> OPLS has multiple definitions for dihedrals using different PN, but GMX only 
> has one line containing the six RB parameters C 0-5.   If someone in the list 
> has experience with these conversions, please enlighten me.

IIRC, the trick is *not* to use the Gromacs RB dihedrals, but in stead
define *multiple* 'normal' Gromacs dihedral potentials with different
multiplicities. I'm not sure if all versions (distributions) of Gromacs
actually support multiple dihedrals, they probably do in the .top (i.e.
for grompp), but may not in the .rtp (i.e. for pdb2gmx).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From kay.gottschalk at weizmann.ac.il  Thu Aug  7 09:34:01 2003
From: kay.gottschalk at weizmann.ac.il (Kay Gottschalk)
Date: Thu Aug  7 09:34:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <3F312782.6080207@chem.vu.nl>
Message-ID: <724A793E-C8A9-11D7-B9F8-000393BB411E@weizmann.ac.il>

I have read in the literature that people calculate the rdf of water 
around single water exposed protein atoms (for example to find the 
difference in the hydration shell around carbons and oxygens).  I want 
to do something comparable to that. Now if I just take g_rdf and one 
protein atom which is solvent exposed, I think that g_rdf normalizes 
the number of water molecules that are close to my reference atom 
according to the number that is expected in a sphere with a certain 
radius around the atom with respect to the density of normal water. The 
problem is that most of the atoms' environment is not solvent, but 
other protein atoms. g_rdf therefore finds much less water molecules 
than expected. I believe that I have to compensate for the volume 
around my reference atom that is inaccessible to water. And I don't 
know how to do it.
Hope my problem is stated more clearly now - if not, complain...
Thanks,
Kay.

On Wednesday, August 6, 2003, at 07:06 PM, Anton Feenstra wrote:

> Kay Gottschalk wrote:
>> No problem with manual:) I'd just like to know how people do the rdf 
>> for single surface atoms. There must be some correction for the 
>> protein volume (which excludes water of course) in the sphere-section 
>> for which the density function is calculated. Is there a clever way 
>> to do that in Gromacs? Actually, I am not sure I am making myself 
>> clear here... At any rate, suggestions would be highly appreciated.
>
> You'll have to do some explaining here ;-(
>
> We've used rdf's (in the past) for comparison with e.g. neutron 
> scattering
> for e.g. water. The angle dependence was added to analyze coordination
> shell structure in liquid water. So, no surfaces there, and no protein.
>
> What do you mean by 'single surface atom', and what correction for 
> protein
> volume should there be? It may be that g_sas has an option to calculate
> the protein surface as well as the volume, but it has been upgraded 
> since
> I last used it so I'm not sure.
>
>
> -- 
> Groetjes,
>
> Anton
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> |             | "If You See Me Getting High, Knock Me Down"           |
> |             | (Red Hot Chili Peppers)                               |
> |_____________|_______________________________________________________|
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
>
>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel



From christoph.freudenberger at chemie.uni-ulm.de  Thu Aug  7 09:51:01 2003
From: christoph.freudenberger at chemie.uni-ulm.de (Christoph Freudenberger)
Date: Thu Aug  7 09:51:01 2003
Subject: [gmx-users] g_rdf
References: <724A793E-C8A9-11D7-B9F8-000393BB411E@weizmann.ac.il>
Message-ID: <3F3204C2.3030308@chemie.uni-ulm.de>

Hi Kay.

I'm not sure whether I understood you problem correctly, but if you
want to study solvation around parts of a protein in angular dependence
you might want to consinder using spatial distribution functions (SDF).
I have written a tool to calculate SDF's from gmx trajectories.

Tell me if you want to try it. I will provide the source code.

Kay Gottschalk wrote:
> I have read in the literature that people calculate the rdf of water 
> around single water exposed protein atoms (for example to find the 
> difference in the hydration shell around carbons and oxygens).  I want 
> to do something comparable to that. Now if I just take g_rdf and one 
> protein atom which is solvent exposed, I think that g_rdf normalizes the 
> number of water molecules that are close to my reference atom according 
> to the number that is expected in a sphere with a certain radius around 
> the atom with respect to the density of normal water. The problem is 
> that most of the atoms' environment is not solvent, but other protein 
> atoms. g_rdf therefore finds much less water molecules than expected. I 
> believe that I have to compensate for the volume around my reference 
> atom that is inaccessible to water. And I don't know how to do it.
> Hope my problem is stated more clearly now - if not, complain...
> Thanks,
> Kay.
> 
> On Wednesday, August 6, 2003, at 07:06 PM, Anton Feenstra wrote:
> 
>> Kay Gottschalk wrote:
>>
>>> No problem with manual:) I'd just like to know how people do the rdf 
>>> for single surface atoms. There must be some correction for the 
>>> protein volume (which excludes water of course) in the sphere-section 
>>> for which the density function is calculated. Is there a clever way 
>>> to do that in Gromacs? Actually, I am not sure I am making myself 
>>> clear here... At any rate, suggestions would be highly appreciated.
>>
>>
>> You'll have to do some explaining here ;-(
>>
>> We've used rdf's (in the past) for comparison with e.g. neutron 
>> scattering
>> for e.g. water. The angle dependence was added to analyze coordination
>> shell structure in liquid water. So, no surfaces there, and no protein.
>>
>> What do you mean by 'single surface atom', and what correction for 
>> protein
>> volume should there be? It may be that g_sas has an option to calculate
>> the protein surface as well as the volume, but it has been upgraded since
>> I last used it so I'm not sure.
>>
>>
>> -- 
>> Groetjes,
>>
>> Anton
>>  _____________ _______________________________________________________
>> |             |                                                       |
>> |  _   _  ___,| K. Anton Feenstra                                     |
>> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
>> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
>> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
>> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
>> |             | "If You See Me Getting High, Knock Me Down"           |
>> |             | (Red Hot Chili Peppers)                               |
>> |_____________|_______________________________________________________|
>>
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>>
>>
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Tel: ++972-8-9343639
> Herzl St. 1
> Rehovot 76100
> Israel
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> 

-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785



From kay.gottschalk at weizmann.ac.il  Thu Aug  7 10:31:01 2003
From: kay.gottschalk at weizmann.ac.il (Kay Gottschalk)
Date: Thu Aug  7 10:31:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <3F3204C2.3030308@chemie.uni-ulm.de>
Message-ID: <5B3643F4-C8B1-11D7-B9F8-000393BB411E@weizmann.ac.il>

Hi Christoph,

danke fuer das Angebot! I'd like to try it. But perhaps I should 
restate my problem to make it (even more:)) clear: The relative 
probability of finding a water water molecule at a given distance r is 
(approximately as stated in the manual)

g(r) = <N(r)>/(4*pi*r^2*dr*rho), where N(r) is the number of water in a 
sperical shell (4*pi*r^2*dr), normalized by the water density rho. 
However, this is only true for symmetrical systems. The problem in my 
case is that the protein excludes water from certain regions, thus I 
have a assymetrical system. Therefore, the spherical shell is not the 
correct volume over which to normalize the function.
Cheers,
Kay.

On Thursday, August 7, 2003, at 10:50 AM, Christoph Freudenberger wrote:

> christoph.freudenberger at chemie.uni-ulm.de
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel



From ygmu at theochem.uni-frankfurt.de  Thu Aug  7 17:42:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Thu Aug  7 17:42:01 2003
Subject: [gmx-users] paralel scaleing
In-Reply-To: <1060071056.3122.44.camel@h28n2fls34o1123.telia.com>
Message-ID: <Pine.LNX.4.44.0308071730100.30660-100000@marge.theochem.uni-frankfurt.de>

I try gromacs on 4 cpus (2 nodes Pentium linux with Myrinet link),
unfortunately, it runs nearly the same speed as in 2 cpus (1 node)
I check the output , here is the output in log file:


               (Mnbf/s)   (GFlops) (ps/NODE hour) (NODE hour/ns)
Performance:     26.848      1.938     30.782     32.486
Detailed load balancing info in percentage of average

Type        NODE:  0   1   2   3 Scaling
---------------------------------------
             LJ:396   0   0   3     25%
          LJ(S):  0   0 386  13     25%
   LJ + Coulomb:400   0   0   0     25%
LJ + Coulomb(T):386   0   0  13     25%
LJ + Coulomb(T)(S): 94  97 110  97     90%
Innerloop-Iatom: 88  82  94 134     74%
Spread Q Bspline: 99  99 100  99     99%
Gather F Bspline: 99  99 100  99     99%
         3D-FFT:100 100 100 100    100%
      Solve PME:100 100 100 100    100%
       NS-Pairs: 98  95 108  97     92%
   Reset In Box: 99  99 100  99     99%
        Shift-X:100 100 100  99     99%
         CG-CoM: 95 101 101 101     98%
     Sum Forces:100 100 100  99     99%
          Bonds:400   0   0   0     25%
         Angles:400   0   0   0     25%
        Propers:400   0   0   0     25%
   RB-Dihedrals:400   0   0   0     25%
   Dist. Restr.:400   0   0   0     25%
         Virial: 99  99 100  99     99%
         Update: 99  99 100  99     99%
        Stop-CM: 99  99 100  99     99%
     P-Coupling: 99  99 100  99     99%
      Calc-Ekin: 99  99 100  99     99%
          Lincs:400   0   0   0     25%
      Lincs-Mat:400   0   0   0     25%
        Shake-V: 99  99 100  99     99%
      Shake-Vir: 99  99 100  99     99%
         Settle: 91 102 102 102     97%
         Dummy2:400   0   0   0     25%

    Total Force:103  94 106  94     93%


    Total Shake: 95 101 101 101     98%

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Compared with 2 cpus (1 nodes) :


               (Mnbf/s)   (GFlops) (ps/NODE hour) (NODE hour/ns)
Performance:     23.269      1.638     26.726     37.417

Detailed load balancing info in percentage of average
Type        NODE:  0   1 Scaling
-------------------------------
             LJ:198   1     50%
          LJ(S):  0 200     50%
   LJ + Coulomb:200   0     50%
LJ + Coulomb(T):193   6     51%
LJ + Coulomb(T)(S): 95 104     95%
Innerloop-Iatom: 85 114     87%
Spread Q Bspline:100  99     99%
Gather F Bspline:100  99     99%
         3D-FFT:100 100    100%
      Solve PME:100 100    100%
       NS-Pairs: 97 102     97%
   Reset In Box:100  99     99%
        Shift-X:100  99     99%
         CG-CoM: 98 101     98%
     Sum Forces:100  99     99%
          Bonds:200   0     50%
         Angles:200   0     50%
        Propers:200   0     50%
   RB-Dihedrals:200   0     50%
   Dist. Restr.:200   0     50%
         Virial:100  99     99%
         Update:100  99     99%
        Stop-CM:100  99     99%
     P-Coupling:100  99     99%
      Calc-Ekin:100  99     99%
          Lincs:200   0     50%
      Lincs-Mat:200   0     50%
        Shake-V:100  99     99%
      Shake-Vir:100  99     99%
         Settle: 97 102     97%
         Dummy2:200   0     50%

    Total Force: 99 100     99%


    Total Shake: 98 101     98%


Total Scaling: 99% of max performance

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

Here I found that the calculations of LJ parts which consuming lots of
cpus are not paralleled at all. Maybe this is the reasons why scaling
factor  is not increaded greatly from 2 cpus to 4 cpus.
DO you agree with me ?
How to improve ?
I use gromacs 3.1.4.

Yuguang




From spoel at xray.bmc.uu.se  Thu Aug  7 17:54:01 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Thu Aug  7 17:54:01 2003
Subject: [gmx-users] paralel scaleing
In-Reply-To: <Pine.LNX.4.44.0308071730100.30660-100000@marge.theochem.uni-frankfurt.de>
References: 	 <Pine.LNX.4.44.0308071730100.30660-100000@marge.theochem.uni-frankfurt.de>
Message-ID: <1060271456.18288.106.camel@werkman.bmc.uu.se>

On Thu, 2003-08-07 at 17:41, Yuguang Mu wrote:
> I try gromacs on 4 cpus (2 nodes Pentium linux with Myrinet link),
> unfortunately, it runs nearly the same speed as in 2 cpus (1 node)
> I check the output , here is the output in log file:
> 
> 
>                (Mnbf/s)   (GFlops) (ps/NODE hour) (NODE hour/ns)
> Performance:     26.848      1.938     30.782     32.486
> Detailed load balancing info in percentage of average
> 
> Type        NODE:  0   1   2   3 Scaling
> ---------------------------------------
>              LJ:396   0   0   3     25%
>           LJ(S):  0   0 386  13     25%
>    LJ + Coulomb:400   0   0   0     25%
> LJ + Coulomb(T):386   0   0  13     25%
> LJ + Coulomb(T)(S): 94  97 110  97     90%
> Innerloop-Iatom: 88  82  94 134     74%
> Spread Q Bspline: 99  99 100  99     99%
> Gather F Bspline: 99  99 100  99     99%
>          3D-FFT:100 100 100 100    100%
>       Solve PME:100 100 100 100    100%
>        NS-Pairs: 98  95 108  97     92%
>    Reset In Box: 99  99 100  99     99%
>         Shift-X:100 100 100  99     99%
>          CG-CoM: 95 101 101 101     98%
>      Sum Forces:100 100 100  99     99%
>           Bonds:400   0   0   0     25%
>          Angles:400   0   0   0     25%
>         Propers:400   0   0   0     25%
>    RB-Dihedrals:400   0   0   0     25%
>    Dist. Restr.:400   0   0   0     25%
>          Virial: 99  99 100  99     99%
>          Update: 99  99 100  99     99%
>         Stop-CM: 99  99 100  99     99%
>      P-Coupling: 99  99 100  99     99%
>       Calc-Ekin: 99  99 100  99     99%
>           Lincs:400   0   0   0     25%
>       Lincs-Mat:400   0   0   0     25%
>         Shake-V: 99  99 100  99     99%
>       Shake-Vir: 99  99 100  99     99%
>          Settle: 91 102 102 102     97%
>          Dummy2:400   0   0   0     25%
> 
>     Total Force:103  94 106  94     93%
> 
> 
>     Total Shake: 95 101 101 101     98%
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Compared with 2 cpus (1 nodes) :
> 
> 
>                (Mnbf/s)   (GFlops) (ps/NODE hour) (NODE hour/ns)
> Performance:     23.269      1.638     26.726     37.417
> 
> Detailed load balancing info in percentage of average
> Type        NODE:  0   1 Scaling
> -------------------------------
>              LJ:198   1     50%
>           LJ(S):  0 200     50%
>    LJ + Coulomb:200   0     50%
> LJ + Coulomb(T):193   6     51%
> LJ + Coulomb(T)(S): 95 104     95%
> Innerloop-Iatom: 85 114     87%
> Spread Q Bspline:100  99     99%
> Gather F Bspline:100  99     99%
>          3D-FFT:100 100    100%
>       Solve PME:100 100    100%
>        NS-Pairs: 97 102     97%
>    Reset In Box:100  99     99%
>         Shift-X:100  99     99%
>          CG-CoM: 98 101     98%
>      Sum Forces:100  99     99%
>           Bonds:200   0     50%
>          Angles:200   0     50%
>         Propers:200   0     50%
>    RB-Dihedrals:200   0     50%
>    Dist. Restr.:200   0     50%
>          Virial:100  99     99%
>          Update:100  99     99%
>         Stop-CM:100  99     99%
>      P-Coupling:100  99     99%
>       Calc-Ekin:100  99     99%
>           Lincs:200   0     50%
>       Lincs-Mat:200   0     50%
>         Shake-V:100  99     99%
>       Shake-Vir:100  99     99%
>          Settle: 97 102     97%
>          Dummy2:200   0     50%
> 
>     Total Force: 99 100     99%
> 
> 
>     Total Shake: 98 101     98%
> 
> 
> Total Scaling: 99% of max performance
> 
> $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
> 
> Here I found that the calculations of LJ parts which consuming lots of
> cpus are not paralleled at all. Maybe this is the reasons why scaling
> factor  is not increaded greatly from 2 cpus to 4 cpus.
> DO you agree with me ?
> How to improve ?
> I use gromacs 3.1.4.

PME scaling is poor, but it depends on your system size too.

Most of the work is in the LJ(S) solvent loops though, so don't worry
about the other term.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From bgroot at gwdg.de  Thu Aug  7 17:59:01 2003
From: bgroot at gwdg.de (Bert de Groot)
Date: Thu Aug  7 17:59:01 2003
Subject: [gmx-users] paralel scaleing
References: <Pine.LNX.4.44.0308071730100.30660-100000@marge.theochem.uni-frankfurt.de> <1060271456.18288.106.camel@werkman.bmc.uu.se>
Message-ID: <3F327701.80476B5A@gwdg.de>

David van der Spoel wrote:
> 
> On Thu, 2003-08-07 at 17:41, Yuguang Mu wrote:
> > I try gromacs on 4 cpus (2 nodes Pentium linux with Myrinet link),
> > unfortunately, it runs nearly the same speed as in 2 cpus (1 node)
> > I check the output , here is the output in log file:
> >
> >
> >                (Mnbf/s)   (GFlops) (ps/NODE hour) (NODE hour/ns)
> > Performance:     26.848      1.938     30.782     32.486
> > Detailed load balancing info in percentage of average
> >
> > Type        NODE:  0   1   2   3 Scaling
> > ---------------------------------------
> >              LJ:396   0   0   3     25%
> >           LJ(S):  0   0 386  13     25%
> >    LJ + Coulomb:400   0   0   0     25%
> > LJ + Coulomb(T):386   0   0  13     25%
> > LJ + Coulomb(T)(S): 94  97 110  97     90%
> > Innerloop-Iatom: 88  82  94 134     74%
> > Spread Q Bspline: 99  99 100  99     99%
> > Gather F Bspline: 99  99 100  99     99%
> >          3D-FFT:100 100 100 100    100%
> >       Solve PME:100 100 100 100    100%
> >        NS-Pairs: 98  95 108  97     92%
> >    Reset In Box: 99  99 100  99     99%
> >         Shift-X:100 100 100  99     99%
> >          CG-CoM: 95 101 101 101     98%
> >      Sum Forces:100 100 100  99     99%
> >           Bonds:400   0   0   0     25%
> >          Angles:400   0   0   0     25%
> >         Propers:400   0   0   0     25%
> >    RB-Dihedrals:400   0   0   0     25%
> >    Dist. Restr.:400   0   0   0     25%
> >          Virial: 99  99 100  99     99%
> >          Update: 99  99 100  99     99%
> >         Stop-CM: 99  99 100  99     99%
> >      P-Coupling: 99  99 100  99     99%
> >       Calc-Ekin: 99  99 100  99     99%
> >           Lincs:400   0   0   0     25%
> >       Lincs-Mat:400   0   0   0     25%
> >         Shake-V: 99  99 100  99     99%
> >       Shake-Vir: 99  99 100  99     99%
> >          Settle: 91 102 102 102     97%
> >          Dummy2:400   0   0   0     25%
> >
> >     Total Force:103  94 106  94     93%
> >
> >
> >     Total Shake: 95 101 101 101     98%
> >
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > Compared with 2 cpus (1 nodes) :
> >
> >
> >                (Mnbf/s)   (GFlops) (ps/NODE hour) (NODE hour/ns)
> > Performance:     23.269      1.638     26.726     37.417
> >
> > Detailed load balancing info in percentage of average
> > Type        NODE:  0   1 Scaling
> > -------------------------------
> >              LJ:198   1     50%
> >           LJ(S):  0 200     50%
> >    LJ + Coulomb:200   0     50%
> > LJ + Coulomb(T):193   6     51%
> > LJ + Coulomb(T)(S): 95 104     95%
> > Innerloop-Iatom: 85 114     87%
> > Spread Q Bspline:100  99     99%
> > Gather F Bspline:100  99     99%
> >          3D-FFT:100 100    100%
> >       Solve PME:100 100    100%
> >        NS-Pairs: 97 102     97%
> >    Reset In Box:100  99     99%
> >         Shift-X:100  99     99%
> >          CG-CoM: 98 101     98%
> >      Sum Forces:100  99     99%
> >           Bonds:200   0     50%
> >          Angles:200   0     50%
> >         Propers:200   0     50%
> >    RB-Dihedrals:200   0     50%
> >    Dist. Restr.:200   0     50%
> >          Virial:100  99     99%
> >          Update:100  99     99%
> >         Stop-CM:100  99     99%
> >      P-Coupling:100  99     99%
> >       Calc-Ekin:100  99     99%
> >           Lincs:200   0     50%
> >       Lincs-Mat:200   0     50%
> >         Shake-V:100  99     99%
> >       Shake-Vir:100  99     99%
> >          Settle: 97 102     97%
> >          Dummy2:200   0     50%
> >
> >     Total Force: 99 100     99%
> >
> >
> >     Total Shake: 98 101     98%
> >
> >
> > Total Scaling: 99% of max performance
> >
> > $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
> >
> > Here I found that the calculations of LJ parts which consuming lots of
> > cpus are not paralleled at all. Maybe this is the reasons why scaling
> > factor  is not increaded greatly from 2 cpus to 4 cpus.
> > DO you agree with me ?
> > How to improve ?
> > I use gromacs 3.1.4.
> 
> PME scaling is poor, but it depends on your system size too.
> 

on the other hand, with myrinet scaling should be considerably better.
Are you sure that you're actually making full use of the hardware?
(ie is the scaling at least better (for that system) than for fast ethernet?)

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________


From ygmu at theochem.uni-frankfurt.de  Thu Aug  7 18:19:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Thu Aug  7 18:19:01 2003
Subject: [gmx-users] paralel scaleing
In-Reply-To: <3F327701.80476B5A@gwdg.de>
Message-ID: <Pine.LNX.4.44.0308071814300.31945-100000@marge.theochem.uni-frankfurt.de>

Here I found a strange message after grompp: (in 4 cpu with myrinet):


perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = (unset),
        LC_ALL = (unset),
        LC_NUMERIC = "C",
        LANG = "en_EN.ISO-8859-1"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").



NNODES=4, MYRANK=1, HOSTNAME=node28
NODEID=1 argc=13
NNODES=4, MYRANK=2, HOSTNAME=node29
NODEID=2 argc=13
NNODES=4, MYRANK=3, HOSTNAME=node29
NODEID=3 argc=13
NNODES=4, MYRANK=0, HOSTNAME=node28
NODEID=0 argc=13




From ygmu at theochem.uni-frankfurt.de  Thu Aug  7 18:21:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Thu Aug  7 18:21:01 2003
Subject: [gmx-users] paralel scaleing
In-Reply-To: <1060271456.18288.106.camel@werkman.bmc.uu.se>
Message-ID: <Pine.LNX.4.44.0308071818450.32021-100000@marge.theochem.uni-frankfurt.de>

> PME scaling is poor, but it depends on your system size too.
>
> Most of the work is in the LJ(S) solvent loops though, so don't worry
> about the other term.
>
>
> --


I agree with you, but why the  LJ(S) parts only calculated in one cpu,
so the scaling for 4 cpu is 25% , and for 2 cpu is 50% ?



From ygmu at theochem.uni-frankfurt.de  Thu Aug  7 20:17:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Thu Aug  7 20:17:01 2003
Subject: [gmx-users] paralel scaleing
In-Reply-To: <3F327701.80476B5A@gwdg.de>
Message-ID: <Pine.LNX.4.31.0308072014060.24973-100000@lisa.theochem.uni-frankfurt.de>

When I swith on the flag in paralel running

domain-decomposition     = yes

It fails in:

Fatal error: ci = -1 should be in 0 .. 1727 [FILE nsgrid.c, LINE 210]
Error on node 1, will try to stop all the nodes
Fatal error: ci = -1 should be in 0 .. 1727 [FILE nsgrid.c, LINE 210]
Error on node 0, will try to stop all the nodes
----------------------------------------------------------------------------


what's reason ?

Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711




From spoel at xray.bmc.uu.se  Thu Aug  7 21:16:02 2003
From: spoel at xray.bmc.uu.se (David)
Date: Thu Aug  7 21:16:02 2003
Subject: [gmx-users] paralel scaleing
In-Reply-To: <Pine.LNX.4.44.0308071818450.32021-100000@marge.theochem.uni-frankfurt.de>
References: 	 <Pine.LNX.4.44.0308071818450.32021-100000@marge.theochem.uni-frankfurt.de>
Message-ID: <1060284012.1747.1.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-07 at 18:20, Yuguang Mu wrote:
> > PME scaling is poor, but it depends on your system size too.
> >
> > Most of the work is in the LJ(S) solvent loops though, so don't worry
> > about the other term.
> >
> >
> > --
> 
> 
> I agree with you, but why the  LJ(S) parts only calculated in one cpu,
> so the scaling for 4 cpu is 25% , and for 2 cpu is 50% ?
First LJ is your protein, or whatever, and the total count is very low
as well, negligable compared to solvent.

>    are supported and installed on your system.
>perl: warning: Falling back to the standard locale ("C").

The Perl message has to with internationalization on your machine and
nothing with gromacs.

Domain decomposition is not implemented yet.


> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Thu Aug  7 21:18:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Thu Aug  7 21:18:00 2003
Subject: [gmx-users] paralel scaleing
In-Reply-To: <3F327701.80476B5A@gwdg.de>
References: 	 <Pine.LNX.4.44.0308071730100.30660-100000@marge.theochem.uni-frankfurt.de>
	 <1060271456.18288.106.camel@werkman.bmc.uu.se>  <3F327701.80476B5A@gwdg.de>
Message-ID: <1060284107.1748.4.camel@h28n2fls34o1123.telia.com>

O> >
> > > Here I found that the calculations of LJ parts which consuming lots of
> > > cpus are not paralleled at all. Maybe this is the reasons why scaling
> > > factor  is not increaded greatly from 2 cpus to 4 cpus.
> > > DO you agree with me ?
> > > How to improve ?
> > > I use gromacs 3.1.4.
> > 
> > PME scaling is poor, but it depends on your system size too.
> > 
> 
> on the other hand, with myrinet scaling should be considerably better.
> Are you sure that you're actually making full use of the hardware?
> (ie is the scaling at least better (for that system) than for fast ethernet?)
> 

That's true, and I've found that with Scali I do get some speedup up to
8 processors for a 80000 atom system. However, it is strongly system
dependent. 

> Bert
> 
> ____________________________________________________________________________
> Dr. Bert de Groot
> 
> Max Planck Institute for Biophysical Chemistry
> Theoretical molecular biophysics group
> Am Fassberg 11 
> 37077 Goettingen, Germany
> 
> tel: +49-551-2011306, fax: +49-551-2011089
> 
> email: bgroot at gwdg.de
> http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
> ____________________________________________________________________________
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From mrshirts at stanford.edu  Thu Aug  7 22:29:01 2003
From: mrshirts at stanford.edu (Michael Shirts)
Date: Thu Aug  7 22:29:01 2003
Subject: [gmx-users] Removal of angular velocity
In-Reply-To: <20030730170001.21520.35255.Mailman@hawk.theophys.kth.se>
Message-ID: <Pine.GSO.4.44.0308071325390.23404-100000@elaine28.Stanford.EDU>

Hi, all-

If I understand the code correctly, GROMACS removes center of mass angular
momenum for periodic boundary conditions.  Is this the case?  If so, what is
the rationale for this?  Periodic boundary conditions are not isotropic for
rotations, so I wouldn't think that it would be a good idea.

Thanks,
Michael Shirts
Pande Group
Stanford University




From spoel at xray.bmc.uu.se  Thu Aug  7 22:39:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Thu Aug  7 22:39:00 2003
Subject: [gmx-users] Removal of angular velocity
In-Reply-To: <Pine.GSO.4.44.0308071325390.23404-100000@elaine28.Stanford.EDU>
References: <Pine.GSO.4.44.0308071325390.23404-100000@elaine28.Stanford.EDU>
Message-ID: <1060289015.1748.8.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-07 at 22:28, Michael Shirts wrote:
> Hi, all-
> 
> If I understand the code correctly, GROMACS removes center of mass angular
> momenum for periodic boundary conditions.  Is this the case?  If so, what is
> the rationale for this?  Periodic boundary conditions are not isotropic for
> rotations, so I wouldn't think that it would be a good idea.
> 
He he... this is why it's optional... You could have two groups, like
two molecules in vacuum that you would want to stop the rotation of. No
clue what it would be good for, but stranger things have been done.


> Thanks,
> Michael Shirts
> Pande Group
> Stanford University
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From lindahl at stanford.edu  Thu Aug  7 22:49:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Thu Aug  7 22:49:01 2003
Subject: [gmx-users] Removal of angular velocity
In-Reply-To: <1060289015.1748.8.camel@h28n2fls34o1123.telia.com>
Message-ID: <467C527A-C918-11D7-84BA-000A95A099E0@stanford.edu>

Just to clarify -

Unless David or Berk changed it recently: in contrast to linear  
momentum, angular momentum is not removed by default, but you can turn  
it on.

Cheers,

Erik


On Thursday, August 7, 2003, at 01:43 PM, David wrote:

> On Thu, 2003-08-07 at 22:28, Michael Shirts wrote:
>> Hi, all-
>>
>> If I understand the code correctly, GROMACS removes center of mass  
>> angular
>> momenum for periodic boundary conditions.  Is this the case?  If so,  
>> what is
>> the rationale for this?  Periodic boundary conditions are not  
>> isotropic for
>> rotations, so I wouldn't think that it would be a good idea.
>>
> He he... this is why it's optional... You could have two groups, like
> two molecules in vacuum that you would want to stop the rotation of. No
> clue what it would be good for, but stranger things have been done.
>
>
>> Thanks,
>> Michael Shirts
>> Pande Group
>> Stanford University
>>
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> --  
> Groeten, David.
> _______________________________________________________________________ 
> _
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> +
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From vraut at CLEMSON.EDU  Thu Aug  7 23:51:01 2003
From: vraut at CLEMSON.EDU (Vivek Raut)
Date: Thu Aug  7 23:51:01 2003
Subject: [gmx-users] how to shift the peptide towards the bottom of the box??
Message-ID: <5.1.1.5.2.20030807174606.00a659d8@mail.clemson.edu>

hi,

i have a peptide (2.gro)

i build the box around it by giving command: editconf -f 1.gro -o 2.gro -bt 
tric -box 3.5 6.0 4.23 -angles 90 90 90

when i solvate the peptide by the 'genbox' command, i see the peptide at 
the center of the box. i want that peptide to be at the bottom of that my 
instead of center. what commands should i add to the commandline ??

Thanks,
vivek

-------------------------------------------------------------------------------------------------------------------------------------------
Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
--------------------------------------------------------------------------------------------------------------------------------------------



From periole at inka.mssm.edu  Thu Aug  7 23:57:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Thu Aug  7 23:57:01 2003
Subject: [gmx-users] how to shift the peptide towards the bottom of the box??
References: <5.1.1.5.2.20030807174606.00a659d8@mail.clemson.edu>
Message-ID: <010201c35d2e$b47437e0$d83a4a86@fox>

I don;t think there is any option to do that ! What about working on the
file .gro and moving the all peptide on the z (or x or y) axe by
substracting
the distance you want to move it to the z (or x or y) coordinates ?

XAvier



From nanyu101 at sina.com  Fri Aug  8 03:37:00 2003
From: nanyu101 at sina.com (nanyu101)
Date: Fri Aug  8 03:37:00 2003
Subject: [gmx-users] PME problem 2!!
Message-ID: <20030808013554.5645.qmail@sina.com>

Dear gmx-users,
  Thanks for David and Xavier Periole 's prompt reply.

Firstly, I have tried to use cutoff 1.2 just as Xavier Periole told, but the same problem happened with " 15848 Segmentation fault".

Secondly, I have just installation my FFTW with double precision.And I didn't find that Gromacs should be installed with double precision in installation web.

I have run with pme model in MD after with cut-off in minimization, the same problem happened with " 15899 Segmentation fault".

 Thanks for your kind assistant.

Best wishes,
Xianhui Wu

______________________________________
Best wishes,
nanyu
===================================================================
????9???????????????????????? (http://mail.sina.com.cn)


From dallas.warren at vcp.monash.edu.au  Fri Aug  8 06:40:01 2003
From: dallas.warren at vcp.monash.edu.au (Dallas Warren)
Date: Fri Aug  8 06:40:01 2003
Subject: [gmx-users] get_index
Message-ID: <5.1.0.14.2.20030808123323.02240fa8@pop.ozhosting.com>

Quick Q, where can I find the get_index and rd_index routines?

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
--------------------------------------------------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-------------- next part --------------
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From feenstra at chem.vu.nl  Fri Aug  8 09:08:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Fri Aug  8 09:08:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <5B3643F4-C8B1-11D7-B9F8-000393BB411E@weizmann.ac.il>
References: <5B3643F4-C8B1-11D7-B9F8-000393BB411E@weizmann.ac.il>
Message-ID: <3F327297.6050307@chem.vu.nl>

Kay Gottschalk wrote:
> Hi Christoph,
> 
> danke fuer das Angebot! I'd like to try it. But perhaps I should restate 
> my problem to make it (even more:)) clear: The relative probability of 
> finding a water water molecule at a given distance r is (approximately 
> as stated in the manual)
> 
> g(r) = <N(r)>/(4*pi*r^2*dr*rho), where N(r) is the number of water in a 
> sperical shell (4*pi*r^2*dr), normalized by the water density rho. 
> However, this is only true for symmetrical systems. The problem in my 
> case is that the protein excludes water from certain regions, thus I 
> have a assymetrical system. Therefore, the spherical shell is not the 
> correct volume over which to normalize the function.

Hmm, I'm not sure actually how it is implemented. It could be either as a
distribution function, which is normalized to an integral of 1, or it is
normalized to a bulk density (i.e. at 'infinite' or 'large' distances) of 1,
which is taken from your actual distribution, not an 'external' reference
value. In any case, there is no normalization to a 'reference' average water
density (which would also be pressure & temperature dependent, and water
model dependent as well).

In either case, I believe three columns are written in the output (.xvg)
file, first the distance, then the normalized rdf and finally the 'raw'
numbers (if not, it would be straightforward to add to the source code).
If you type 'xmgrace -nxy rdf.xvg', you will see all available plots in
the file.



-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From spoel at xray.bmc.uu.se  Fri Aug  8 09:11:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Fri Aug  8 09:11:00 2003
Subject: [gmx-users] how to shift the peptide towards the bottom of the
	box??
In-Reply-To: <5.1.1.5.2.20030807174606.00a659d8@mail.clemson.edu>
References: <5.1.1.5.2.20030807174606.00a659d8@mail.clemson.edu>
Message-ID: <1060326927.2144.16.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-07 at 23:49, Vivek Raut wrote:
> hi,
> 
> i have a peptide (2.gro)
> 
> i build the box around it by giving command: editconf -f 1.gro -o 2.gro -bt 
> tric -box 3.5 6.0 4.23 -angles 90 90 90
> 
> when i solvate the peptide by the 'genbox' command, i see the peptide at 
> the center of the box. i want that peptide to be at the bottom of that my 
> instead of center. what commands should i add to the commandline ??
> 
If your box is 4 x 4 x 4 you could do:
editcont -center 2 2 0

> Thanks,
> vivek
> 
> -------------------------------------------------------------------------------------------------------------------------------------------
> Vivek Raut
> Graduate Research Assistant
> Department of Bioengineering
> Clemson University
> Clemson, SC- 29631. USA
> Email: vraut at clemson.edu
> Phone: 864-650-1431
> --------------------------------------------------------------------------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Fri Aug  8 09:14:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Fri Aug  8 09:14:01 2003
Subject: [gmx-users] get_index
In-Reply-To: <5.1.0.14.2.20030808123323.02240fa8@pop.ozhosting.com>
References: <5.1.0.14.2.20030808123323.02240fa8@pop.ozhosting.com>
Message-ID: <1060327070.2142.20.camel@h28n2fls34o1123.telia.com>

On Fri, 2003-08-08 at 04:37, Dallas Warren wrote:
> Quick Q, where can I find the get_index and rd_index routines?
> 

Depends, in 3.1.4 it would be rdgroup.c in CVS it has been renamed to
index.c

grep get_index gmx/src/gmxlib/*c

gmx/src/gmxlib/index.c:void get_index(t_atoms *atoms, char *fnm, int
ngrps,
gmx/src/gmxlib/rdgroup.c:void get_index(t_atoms *atoms, char *fnm, int
ngrps,
[
> Catch ya,
> 
> 
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Fri Aug  8 09:22:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Fri Aug  8 09:22:00 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <3F327297.6050307@chem.vu.nl>
References: <5B3643F4-C8B1-11D7-B9F8-000393BB411E@weizmann.ac.il>
	 <3F327297.6050307@chem.vu.nl>
Message-ID: <1060327568.2144.26.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-07 at 17:39, Anton Feenstra wrote:
> Kay Gottschalk wrote:
> > Hi Christoph,
> > 
> > danke fuer das Angebot! I'd like to try it. But perhaps I should restate 
> > my problem to make it (even more:)) clear: The relative probability of 
> > finding a water water molecule at a given distance r is (approximately 
> > as stated in the manual)
> > 
> > g(r) = <N(r)>/(4*pi*r^2*dr*rho), where N(r) is the number of water in a 
> > sperical shell (4*pi*r^2*dr), normalized by the water density rho. 
> > However, this is only true for symmetrical systems. The problem in my 
> > case is that the protein excludes water from certain regions, thus I 
> > have a assymetrical system. Therefore, the spherical shell is not the 
> > correct volume over which to normalize the function.
> 
> Hmm, I'm not sure actually how it is implemented. It could be either as a
> distribution function, which is normalized to an integral of 1, or it is
> normalized to a bulk density (i.e. at 'infinite' or 'large' distances) of 1,
> which is taken from your actual distribution, not an 'external' reference
> value. In any case, there is no normalization to a 'reference' average water
> density (which would also be pressure & temperature dependent, and water
> model dependent as well).
> 
> In either case, I believe three columns are written in the output (.xvg)
> file, first the distance, then the normalized rdf and finally the 'raw'
> numbers (if not, it would be straightforward to add to the source code).
> If you type 'xmgrace -nxy rdf.xvg', you will see all available plots in
> the file.

I don't think there is any reason to renormalize, the normalization is
done based on the number of water molecules (oxygens) in the
computational box, and since your site of interest is partially occluded
by protein the number of bound water molecules will not be the same as
for a particle in solution. 

Try to take the integral of the RDF (using Int 4 pi r^2 g(r) from 0 to
the first minimum), that will give you the average number of hydrogen
bonded water molecules.



-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From arvid at fmp-berlin.de  Fri Aug  8 09:39:00 2003
From: arvid at fmp-berlin.de (Arvid Soederhaell)
Date: Fri Aug  8 09:39:00 2003
Subject: [gmx-users] equilibration
In-Reply-To: <20030807204901.8457.72666.Mailman@hawk.theophys.kth.se>
Message-ID: <Pine.SGI.3.96.1030808090333.24858M-100000@gretchen.fmp-berlin.de>

Hi all
I am trying to equilibrate a membrane-peptide-water-ion system but it
doesn't work. Gromacs is quite new to me so the questions might be stupid.
The system should already be quite well equilibrated since it comes from
dynamics run using amber. The only thing that is done is making a new
periodic box and adding hydrogens. 

I have tested to do a steepest descen minimization and the error message
in the .log file is:  
--------------------------------------------------------------------
Stepsize too small (6.10352e-07 nm)Converged to machine precision, 
but not to the requested precision (1) 
You might need to increase your constraint accuracy, or turn off
constraints alltogether (set constraints = none in mdp file) 

Steepest Descents did not converge in 15 steps
  Potential Energy = nan Maximum force:  1.45952e+10
--------------------------------------------------------------------- I
have set nsteps = 1000, emtol = 1.0 and emstep = 0.01. I really don't get
what the "Stepsize too small (6.1035" etc. means? I have also set the
constraints = none, but nothing changes. 




When I try to make a dynamics simulation instead the system explodes
immediately and I get the following error message after 9 steps: 
----------------------------------------------------------------------
Fatal error: ci = -2147483648 should be in 0 .. 1880 [FILE nsgrid.c, LINE
210]
----------------------------------------------------------------------
When I look at the dynamics trajectory all atoms are out of the box in 2
steps. Even when I use dt = 0.001. 

A question that will be a problem later: I would like to scale the
temperature of the peptide, the lipids and water+ions separately. How
should I formulate this in the .mdp file? (How to put water and ions in
the same group?)
-------------------
tcoupl  = Berendsen 
tc_grps = Protein DPPC (SOL Cl)   ????? 
tau_t   =   0.1    0.1   0.1 
ref_t   =    30     30    30 
----------------------------




The topology file looks like this (Note that in the [molecules] section
I have commented away the "Protein 1" line. If I keep thath line, grompp 
complains and count the number of atoms in the protein twice!!?? The
rw-conn.itp file describes the peptide.):
------------------------------------------------------------------------- 
#include "ffgmx.itp"  
#include "lipid.itp"  
#include "dppc.itp"  
#include "rw-conn.itp" 
#include "ions.itp" 

#ifdef FLEX_SPC 
#include "flexspc.itp"  
#else 
#include "spc.itp"  
#endif

[ system ]  
; name 
PMWI (Peptide Membrane Water Ion) 

[ molecules ] 
; name number 
;Protein 1 
DPPC 64 
SOL 2463 
Cl 3
------------------------------------------------------------------------------


Thanx in advance 
    Arvid Soderhall





From mehmet at suezen.org  Fri Aug  8 10:15:01 2003
From: mehmet at suezen.org (Mehmet Suezen)
Date: Fri Aug  8 10:15:01 2003
Subject: [gmx-users] equilibration
In-Reply-To: <Pine.SGI.3.96.1030808090333.24858M-100000@gretchen.fmp-berlin.de>
Message-ID: <3F0B3F7400014FD4@mta10.wss.scd.yahoo.com>

Hi,
Before trying to minimize, running in NVT ensemble 
some time suitable to your system, might be helpful.
What was the previous ensemble in your dynamic run?
Also changing your geometry of PBC would change 
all the previous coordinates, isn't it? What
about integration time step.

Mehmet

>-- Original Message --
>From: Arvid Soederhaell <arvid at fmp-berlin.de>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] equilibration
>Reply-To: gmx-users at gromacs.org
>Date: Fri, 8 Aug 2003 09:38:36 +0200 (MEDT)
>
>
>Hi all
>I am trying to equilibrate a membrane-peptide-water-ion system but it
>doesn't work. Gromacs is quite new to me so the questions might be stupid.
>The system should already be quite well equilibrated since it comes from
>dynamics run using amber. The only thing that is done is making a new
>periodic box and adding hydrogens. 
>
>I have tested to do a steepest descen minimization and the error message
>in the .log file is:  
>--------------------------------------------------------------------
>Stepsize too small (6.10352e-07 nm)Converged to machine precision, 
>but not to the requested precision (1) 
>You might need to increase your constraint accuracy, or turn off
>constraints alltogether (set constraints = none in mdp file) 
>
>Steepest Descents did not converge in 15 steps
>  Potential Energy = nan Maximum force:  1.45952e+10
>--------------------------------------------------------------------- I
>have set nsteps = 1000, emtol = 1.0 and emstep = 0.01. I really don't get
>what the "Stepsize too small (6.1035" etc. means? I have also set the
>constraints = none, but nothing changes. 
>
>
>
>
>When I try to make a dynamics simulation instead the system explodes
>immediately and I get the following error message after 9 steps: 
>----------------------------------------------------------------------
>Fatal error: ci = -2147483648 should be in 0 .. 1880 [FILE nsgrid.c, LINE
>210]
>----------------------------------------------------------------------
>When I look at the dynamics trajectory all atoms are out of the box in
2
>steps. Even when I use dt = 0.001. 
>
>A question that will be a problem later: I would like to scale the
>temperature of the peptide, the lipids and water+ions separately. How
>should I formulate this in the .mdp file? (How to put water and ions in
>the same group?)
>-------------------
>tcoupl  = Berendsen 
>tc_grps = Protein DPPC (SOL Cl)   ????? 
>tau_t   =   0.1    0.1   0.1 
>ref_t   =    30     30    30 
>----------------------------
>
>
>
>
>The topology file looks like this (Note that in the [molecules] section
>I have commented away the "Protein 1" line. If I keep thath line, grompp
>
>complains and count the number of atoms in the protein twice!!?? The
>rw-conn.itp file describes the peptide.):
>-------------------------------------------------------------------------
>
>#include "ffgmx.itp"  
>#include "lipid.itp"  
>#include "dppc.itp"  
>#include "rw-conn.itp" 
>#include "ions.itp" 
>
>#ifdef FLEX_SPC 
>#include "flexspc.itp"  
>#else 
>#include "spc.itp"  
>#endif
>
>[ system ]  
>; name 
>PMWI (Peptide Membrane Water Ion) 
>
>[ molecules ] 
>; name number 
>;Protein 1 
>DPPC 64 
>SOL 2463 
>Cl 3
>------------------------------------------------------------------------------
>
>
>Thanx in advance 
>    Arvid Soderhall
>
>
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

------------------------------------------------------
Mehmet Suzen  AMInstP
http://www.suzen.org





From gmx3 at hotmail.com  Fri Aug  8 15:36:02 2003
From: gmx3 at hotmail.com (Berk Hess)
Date: Fri Aug  8 15:36:02 2003
Subject: [gmx-users] g_rdf 
Message-ID: <Law11-F124Ywu8fmtEq0001cf6c@hotmail.com>

>Try to take the integral of the RDF (using Int 4 pi r^2 g(r) from 0 to
>the first minimum), that will give you the average number of hydrogen
>bonded water molecules.

The -cn option of g_rdf plots exactly this integral from 0 to r as a 
function of r,
so you can see the number of bound water molecules as a function of the 
distance.

Berk.

_________________________________________________________________
Add photos to your messages with MSN 8. Get 2 months FREE*. 
http://join.msn.com/?page=features/featuredemail



From kay.gottschalk at weizmann.ac.il  Fri Aug  8 15:52:01 2003
From: kay.gottschalk at weizmann.ac.il (Kay Gottschalk)
Date: Fri Aug  8 15:52:01 2003
Subject: [gmx-users] g_rdf
In-Reply-To: <1060327568.2144.26.camel@h28n2fls34o1123.telia.com>
Message-ID: <419F9936-1DD5-11B2-8BB4-000393BB411E@weizmann.ac.il>

Thanks, I'll try that!
Cheers,
K.
On Friday, August 8, 2003, at 10:26 AM, David wrote:

> On Thu, 2003-08-07 at 17:39, Anton Feenstra wrote:
>> Kay Gottschalk wrote:
>>> Hi Christoph,
>>>
>>> danke fuer das Angebot! I'd like to try it. But perhaps I should  
>>> restate
>>> my problem to make it (even more:)) clear: The relative probability  
>>> of
>>> finding a water water molecule at a given distance r is  
>>> (approximately
>>> as stated in the manual)
>>>
>>> g(r) = <N(r)>/(4*pi*r^2*dr*rho), where N(r) is the number of water  
>>> in a
>>> sperical shell (4*pi*r^2*dr), normalized by the water density rho.
>>> However, this is only true for symmetrical systems. The problem in my
>>> case is that the protein excludes water from certain regions, thus I
>>> have a assymetrical system. Therefore, the spherical shell is not the
>>> correct volume over which to normalize the function.
>>
>> Hmm, I'm not sure actually how it is implemented. It could be either  
>> as a
>> distribution function, which is normalized to an integral of 1, or it  
>> is
>> normalized to a bulk density (i.e. at 'infinite' or 'large'  
>> distances) of 1,
>> which is taken from your actual distribution, not an 'external'  
>> reference
>> value. In any case, there is no normalization to a 'reference'  
>> average water
>> density (which would also be pressure & temperature dependent, and  
>> water
>> model dependent as well).
>>
>> In either case, I believe three columns are written in the output  
>> (.xvg)
>> file, first the distance, then the normalized rdf and finally the  
>> 'raw'
>> numbers (if not, it would be straightforward to add to the source  
>> code).
>> If you type 'xmgrace -nxy rdf.xvg', you will see all available plots  
>> in
>> the file.
>
> I don't think there is any reason to renormalize, the normalization is
> done based on the number of water molecules (oxygens) in the
> computational box, and since your site of interest is partially  
> occluded
> by protein the number of bound water molecules will not be the same as
> for a particle in solution.
>
> Try to take the integral of the RDF (using Int 4 pi r^2 g(r) from 0 to
> the first minimum), that will give you the average number of hydrogen
> bonded water molecules.
>
>
>
> --  
> Groeten, David.
> _______________________________________________________________________ 
> _
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> +
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Tel: ++972-8-9343639
Herzl St. 1
Rehovot 76100
Israel



From sinhvis2 at iit.edu  Fri Aug  8 18:43:01 2003
From: sinhvis2 at iit.edu (Vishal Kumar Sinha)
Date: Fri Aug  8 18:43:01 2003
Subject: [gmx-users] [gmx-users]Running gromacs in parrallel environment.
Message-ID: <4d82584d39a4.4d39a44d8258@iit.edu>

Gmx-users:
I have installed the parallel version of Gromacs in
the sun cluster machine. I have already installed
and configured the LAM-MPI in Sun cluster machine.

I have some question in regard to parralel versions
of MPI
1> Whether parallelism is introduced in FFTW
libraries or in gromacs code .
2> If it is in gromacs code, can it be possible to
explain how it is organized so that which code is
written in parrallel and which in sequential.

Further , I want to run modify demo program so that
I can run it on multiple nodes. Kindly let me know
the changes needed to be made.

Regards
Vishal

Graduate student
IIT Chicago



From periole at inka.mssm.edu  Fri Aug  8 18:54:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Fri Aug  8 18:54:01 2003
Subject: [gmx-users] equilibration
References: <Pine.SGI.3.96.1030808090333.24858M-100000@gretchen.fmp-berlin.de>
Message-ID: <003401c35dcd$821af730$d83a4a86@fox>

> I am trying to equilibrate a membrane-peptide-water-ion system but it
> doesn't work. Gromacs is quite new to me so the questions might be stupid.
> The system should already be quite well equilibrated since it comes from
> dynamics run using amber. The only thing that is done is making a new
> periodic box and adding hydrogens.

1) if your system has been equilibrated in another force field it will need
another
equilibration
2) are you sure it is not taing out hydrogens ?

>
> I have tested to do a steepest descen minimization and the error message
> in the .log file is:
> --------------------------------------------------------------------
> Stepsize too small (6.10352e-07 nm)Converged to machine precision,
> but not to the requested precision (1)
> You might need to increase your constraint accuracy, or turn off
> constraints alltogether (set constraints = none in mdp file)
>
> Steepest Descents did not converge in 15 steps
>   Potential Energy = nan Maximum force:  1.45952e+10
> --------------------------------------------------------------------- I
> have set nsteps = 1000, emtol = 1.0 and emstep = 0.01. I really don't get
> what the "Stepsize too small (6.1035" etc. means? I have also set the
> constraints = none, but nothing changes.
>

There is definitely a problem in your system. The stepsize too small has
been
explained in the list. You'll find it in the archive, see the web site.

>
> When I try to make a dynamics simulation instead the system explodes
> immediately and I get the following error message after 9 steps:
> ----------------------------------------------------------------------
> Fatal error: ci = -2147483648 should be in 0 .. 1880 [FILE nsgrid.c, LINE
> 210]
> ----------------------------------------------------------------------
> When I look at the dynamics trajectory all atoms are out of the box in 2
> steps. Even when I use dt = 0.001.
>

Your system is probably exploding for the same reason the minimization
did not work. Did you minimize in Amber ?

> A question that will be a problem later: I would like to scale the
> temperature of the peptide, the lipids and water+ions separately. How
> should I formulate this in the .mdp file? (How to put water and ions in
> the same group?)
> -------------------
> tcoupl  = Berendsen
> tc_grps = Protein DPPC (SOL Cl)   ?????
> tau_t   =   0.1    0.1   0.1
> ref_t   =    30     30    30
> ----------------------------
>

sounds good.


> The topology file looks like this (Note that in the [molecules] section
> I have commented away the "Protein 1" line. If I keep thath line, grompp
> complains and count the number of atoms in the protein twice!!?? The
> rw-conn.itp file describes the peptide.):
> -------------------------------------------------------------------------
> #include "ffgmx.itp"
> #include "lipid.itp"
> #include "dppc.itp"
> #include "rw-conn.itp"
> #include "ions.itp"
>
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>
> [ system ]
> ; name
> PMWI (Peptide Membrane Water Ion)
>
> [ molecules ]
> ; name number
> ;Protein 1
> DPPC 64
> SOL 2463
> Cl 3
>

Looks like there is a problem in the definition of your system. In your pdb
or gro file
is the order of appeareance protein, dppc, sol and CL ? That could be a
conflict.


hope it helps
XAvier




From YSUN at mie.utoronto.ca  Fri Aug  8 19:46:02 2003
From: YSUN at mie.utoronto.ca (YSUN at mie.utoronto.ca)
Date: Fri Aug  8 19:46:02 2003
Subject: [gmx-users] pull code for speptide
Message-ID: <1060364720.3f33e1b0360c0@webmail.mie.utoronto.ca>


Dear GMX-USERS,

I am trying a pull code on example: speptide (under tutor/speptide).
I applied pulling on a top atom (atom 9) and freeze at a bottom atom (atom 140),

and used 

grompp -f pr.mdp -o prpull3 -c after_em -p speptide -n index.ndx

mdrun -s prpull3.tpr -o prpull3 -c prpull3.gro -e prpull3.edr -g prpull3.log -
pi pull.ppa -pn index.ndx

The error came out:  "floating exception"

Would appreciate if you could help me to identify the problem.

I attached two relevant files (.ppa and .mdp, index file is too big) here for 
your information.

Thanks in advance!

Sun

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From ygmu at theochem.uni-frankfurt.de  Fri Aug  8 19:51:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Fri Aug  8 19:51:01 2003
Subject: [gmx-users] infinite systems
In-Reply-To: <1059644932.27733.17.camel@werkman.bmc.uu.se>
Message-ID: <Pine.LNX.4.31.0308081940450.29914-100000@lisa.theochem.uni-frankfurt.de>

Dear David,
I want to simulate  an infinite system, a small peptide in water
the system is quite small, total 200 atoms.
if I use normal cut-off, the rcut  has to be smaller than box/2 (around 5
A), then the simulated system is nonphysical, due to the small cutoff.
I try to use setenv GMXFULLPBC 1, as:  export GMXFULLPBC=1, then use
rcut=1nm .
But the grompp still say it is a error : rcut > box/2.
What should I do ?


Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On 31 Jul 2003, David van der Spoel wrote:

> On Thu, 2003-07-31 at 11:43, Yuguang Mu wrote:
> > Hi David,
> > What use is the environment variable:
> >  setenv GMXFULLPBC 1
> >
> > Does it means that the cutoff can be larger than the half of a box ?
> > Can it be used in Gromacs 3.1.4 ?
> yes,
>
> it means that infinite systems can be treated as well, because gmx
> computes the periodicity for each interaction separately instead of once
> per molecule (which is faster).
> >
> >
> > Dr. Yuguang Mu
> > Institute for Physical and Theoretical Chemistry
> > J.W. Goethe University Frankfurt am Main
> > Marie Curie Str. 11
> > 60439 Frankfurt/Main, Germany
> > Tel: +49-(0)69-798-29711
> >
> > On 31 Jul 2003, David van der Spoel wrote:
> >
> > > On Thu, 2003-07-31 at 10:38, Yonggang Gao wrote:
> > >
> > > >
> > > > Hi Anton,
> > > >
> > > >
> > > >
> > > > I just select one layer graphite about 432 carbon atoms as solute, and
> > > > the simulation is error when I put it into the water and make it
> > > > equilibrium. Certainly I have done the minimization. And I?m confused
> > > > that it is OK if I put the graphite into vacuum without water and
> > > > simulate it. I don?t know why the water will affect the graphite?s 1-4
> > > > interaction. I try to select two layer graphite about 864 atoms, and
> > > > the same problem. Could you help me?
> > > >
> > > >
> > > >
> > > > Thanks a lot.
> > >
> > >
> > > is this a periodic system? In that case you may want to set an
> > > environment variable:
> > > setenv GMXFULLPBC 1
> > >
> > > and rerun
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Yonggang
> > > >
> > > >
> > > --
> > > Groeten, David.
> > > ________________________________________________________________________
> > > Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> > > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > > phone:	46 18 471 4205		fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From vuissozjm at bluewin.ch  Fri Aug  8 21:33:00 2003
From: vuissozjm at bluewin.ch (jean-marc vuissoz)
Date: Fri Aug  8 21:33:00 2003
Subject: [gmx-users] basic question for a MD run
Message-ID: <0054A49F-C973-11D7-9EA3-000A27B21F4C@bluewin.ch>

hello,

here are some basic question :
a) when I put periodic conditions, does I have to have a neutral charge 
for my system (ie probably putting some ion in the system) ? is there a 
easy way to check the charge of your system once you have it ?

b) I try to equilibrate a system ( a protein with a ligan (also 
protein) in a water box), what type of pressure condition should I put, 
I try with berendsen but after 1.4ns I get an rmsd of the Calpha which 
is between 0.5-0.6 nm (not very good for an equilibration )

best thanks

vuissoz jean-marc



From ichorny at maxwell.compbio.ucsf.edu  Fri Aug  8 21:38:01 2003
From: ichorny at maxwell.compbio.ucsf.edu (Ilya Chorny)
Date: Fri Aug  8 21:38:01 2003
Subject: [gmx-users] Generating Topology File
Message-ID: <1060371434.10459.8.camel@chaos.compbio.ucsf.edu>

I have generated a topology file for the molecule I am interested in
studying using PRODRG. How do I then specify which forcefield to use. I
would like to use OPLS. The Molecule is CH3-(CH2)x-NH3+.

Thanks

Ilya
-- 
----------------------------------------------------------------
Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
Postdoctoral Researcher   University of California-San Francisco
phone: (408)-887-8496     Genentech Hall 600 16th St Box 2240
fax: (415)502-1411        San Francisco, Ca, 94107
            email: ichorny at maxwell.ucsc.edu
----------------------------------------------------------------



From vdava at davapc1.bioch.dundee.ac.uk  Fri Aug  8 22:11:04 2003
From: vdava at davapc1.bioch.dundee.ac.uk (Daan van Aalten)
Date: Fri Aug  8 22:11:04 2003
Subject: [gmx-users] Generating Topology File
In-Reply-To: <1060371434.10459.8.camel@chaos.compbio.ucsf.edu>
Message-ID: <Pine.LNX.4.33.0308082100120.25707-100000@davapc1.bioch.dundee.ac.uk>

Hi Ilya

You can ONLY use the ffgmx2 force field with the PRODRG topologies

cheers

Daan

On 8 Aug 2003, Ilya Chorny wrote:

> I have generated a topology file for the molecule I am interested in
> studying using PRODRG. How do I then specify which forcefield to use. I
> would like to use OPLS. The Molecule is CH3-(CH2)x-NH3+.
>
> Thanks
>
> Ilya
> --
> ----------------------------------------------------------------
> Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
> Postdoctoral Researcher   University of California-San Francisco
> phone: (408)-887-8496     Genentech Hall 600 16th St Box 2240
> fax: (415)502-1411        San Francisco, Ca, 94107
>             email: ichorny at maxwell.ucsc.edu
> ----------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O



From spoel at xray.bmc.uu.se  Fri Aug  8 23:17:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Fri Aug  8 23:17:00 2003
Subject: [gmx-users] basic question for a MD run
In-Reply-To: <0054A49F-C973-11D7-9EA3-000A27B21F4C@bluewin.ch>
References: <0054A49F-C973-11D7-9EA3-000A27B21F4C@bluewin.ch>
Message-ID: <1060377680.8702.3.camel@localhost.localdomain>

On Fri, 2003-08-08 at 09:36, jean-marc vuissoz wrote:
> hello,
> 
> here are some basic question :
> a) when I put periodic conditions, does I have to have a neutral charge 
> for my system (ie probably putting some ion in the system) ? is there a 
> easy way to check the charge of your system once you have it ?
> 
grompp will tell you when it's not neutral

> b) I try to equilibrate a system ( a protein with a ligan (also 
> protein) in a water box), what type of pressure condition should I put, 
> I try with berendsen but after 1.4ns I get an rmsd of the Calpha which 
> is between 0.5-0.6 nm (not very good for an equilibration )
> 
Unless you have a multidomain protein that is too much. If you do have a
multidomain protein you may want to check the RMSD for the individual
domains. 

Pressure coupling at ambient pressure (1 bar) with tau_p = 1-5 ps and
compressibility on the order of 5e-5 should work. You may also start
with position restraints, see tutorial


> best thanks
> 
> vuissoz jean-marc
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From sachin_gursahani at yahoo.com  Sat Aug  9 20:31:01 2003
From: sachin_gursahani at yahoo.com (Sachin Gursahani)
Date: Sat Aug  9 20:31:01 2003
Subject: [gmx-users] Error prb
In-Reply-To: <20030809100002.30407.25973.Mailman@hawk.theophys.kth.se>
Message-ID: <20030809183025.11645.qmail@web80603.mail.yahoo.com>

Dear friends....

I ve this typical error while i was running the
simulation for Cytochrome C...

Fatal error: number of coordinates in coordinate file
(1HRC_b4pr.gro, 10243)
             does not match topology (1HRC.top, 10229)
this error occured after i generated the pr.mdp
file..and while i was running:

grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL}
-o ${MOL}_pr

please anyone let me know how to solve this one ..
.
regards
Sachin

note: ive used the command genion to genion to
generate 7 Cl ions coz the total charge on the system
is +7 and i wanted to make it 0....

the nsteps for mdrun is 150000.



__________________________________
Do you Yahoo!?
SBC Yahoo! DSL - Now only $29.95 per month!
http://sbc.yahoo.com


From Xavier.Periole at physbio.mssm.edu  Sat Aug  9 20:40:02 2003
From: Xavier.Periole at physbio.mssm.edu (Xavier Periole)
Date: Sat Aug  9 20:40:02 2003
Subject: [gmx-users] Error prb
In-Reply-To: <20030809183025.11645.qmail@web80603.mail.yahoo.com>
Message-ID: <A1F8995C-CA55-11D7-853E-0050E41E2965@physbio.mssm.edu>

That is a simple one: the number of atoms defined in your topology
file (topol.top) is different from the number of atoms that are your
conf.gro. You have 14 atoms extra in the conf.gro that are not in the
topology file. Check the missing atoms and include them in the
topology file.

XAvier



On Saturday, August 9, 2003, at 02:30  pm, Sachin Gursahani wrote:

> Dear friends....
>
> I ve this typical error while i was running the
> simulation for Cytochrome C...
>
> Fatal error: number of coordinates in coordinate file
> (1HRC_b4pr.gro, 10243)
>              does not match topology (1HRC.top, 10229)
> this error occured after i generated the pr.mdp
> file..and while i was running:
>
> grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL}
> -o ${MOL}_pr
>
> please anyone let me know how to solve this one ..
> .
> regards
> Sachin
>
> note: ive used the command genion to genion to
> generate 7 Cl ions coz the total charge on the system
> is +7 and i wanted to make it 0....
>
> the nsteps for mdrun is 150000.
>
>
>
> __________________________________
> Do you Yahoo!?
> SBC Yahoo! DSL - Now only $29.95 per month!
> http://sbc.yahoo.com
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From zhangw at sinr.ac.cn  Sun Aug 10 15:46:02 2003
From: zhangw at sinr.ac.cn (zhangwei)
Date: Sun Aug 10 15:46:02 2003
Subject: [gmx-users] A question on simulation carbon nanotubes
Message-ID: <MSG9V6P50NKyYCBklLX00005b3f@msg.sinr.ac.cn>

Hi,everybody,

     I want to simulate carbon nanotubes with gromacs. Within the types of potentials given in Gromacs, I don't know how to construct the bonding interaction in the nanotubes. Could I simulate the bonds in a nanotube with only van de Waals potential? 

	

??????	

????????Wei Zhang
????????zhangw at sinr.ac.cn
??????????2003-08-10




From ajtervo at csc.fi  Sun Aug 10 15:52:01 2003
From: ajtervo at csc.fi (Anu Tervo)
Date: Sun Aug 10 15:52:01 2003
Subject: [gmx-users] Visualizing Gromacs trajectories with InsightII
Message-ID: <Pine.SGI.4.10.10308101640320.33431446-100000@cedar-f.csc.fi>

Dear all,

does anyone know how to visualize Gromacs trajectories with InsightII?
When using Gromacs version 2.0, the thing goes something like:

trjconv -f trajectory.tpb -o trajectory.g87 -nog87box
gtoarc1 system.gro trajectory.g87 trajectory.arc 

but it would be nice to visualize trajectories of newer gromacs versions
as well (currently I'm using Gromacs 3.0.3 but it will be updated soon).
It seems that gtoarc1 has been removed from version 3.0 -> so if someone
knows any other way to generate Insight .arc file it would be nice to
know!

Cheers,
		-Anu





From albert_sun9 at yahoo.com  Sun Aug 10 23:26:01 2003
From: albert_sun9 at yahoo.com (Albert Sun)
Date: Sun Aug 10 23:26:01 2003
Subject: [gmx-users] Topology File
In-Reply-To: <Pine.LNX.4.33.0308082100120.25707-100000@davapc1.bioch.dundee.ac.uk>
Message-ID: <20030810212500.45740.qmail@web21501.mail.yahoo.com>


Dear Users,

I wrote my own  .top  file and  ran the  em.mdp, here are errors 

WARNING 1 [file "try1.top", line 18]:
  Invalid directive atom
WARNING 2 [file "try1.top", line 22]:
  Too few parameters on line (source file toppush.c, line 673)
WARNING 3 [file "try1.top", line 23]:


could you advise me how to avoid the errors?  I  attached my .top here.

Many thanks 

Albert

 

 




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From albert_sun9 at yahoo.com  Sun Aug 10 23:26:03 2003
From: albert_sun9 at yahoo.com (Albert Sun)
Date: Sun Aug 10 23:26:03 2003
Subject: [gmx-users] Topology File
In-Reply-To: <Pine.LNX.4.33.0308082100120.25707-100000@davapc1.bioch.dundee.ac.uk>
Message-ID: <20030810212500.45740.qmail@web21501.mail.yahoo.com>


Dear Users,

I wrote my own  .top  file and  ran the  em.mdp, here are errors 

WARNING 1 [file "try1.top", line 18]:
  Invalid directive atom
WARNING 2 [file "try1.top", line 22]:
  Too few parameters on line (source file toppush.c, line 673)
WARNING 3 [file "try1.top", line 23]:


could you advise me how to avoid the errors?  I  attached my .top here.

Many thanks 

Albert

 

 




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From k24dgyl at morgan.ucs.mun.ca  Mon Aug 11 05:19:01 2003
From: k24dgyl at morgan.ucs.mun.ca (Derrick Guang Yuh Lee)
Date: Mon Aug 11 05:19:01 2003
Subject: [gmx-users] crash 
In-Reply-To: <BAY7-F55f4aulqHFXfU0000d7f9@hotmail.com>
Message-ID: <Pine.OSF.3.95.1030811004602.3417A-100000@plato.ucs.mun.ca>

dear gmx-users

i was just curious if anyone could answer a quick question, when i ran a
simulation it produced two *.pdb file (step0.pdb and step-1.pdb) when i
read the pdb file, the HEADER of step0.pdb stated "crash" and the HEADER
of step-1.pdb stated "one step before crash". obviously this is cases a
bit of concern on my part... so, could anyone fill me in to a possible
cause for this crash? thank you.


sincerley

 - derrick



 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com
 
"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst." 
                                                              - bruce lee



From dallas.warren at vcp.monash.edu.au  Mon Aug 11 06:03:01 2003
From: dallas.warren at vcp.monash.edu.au (Dallas Warren)
Date: Mon Aug 11 06:03:01 2003
Subject: [gmx-users] crash
In-Reply-To: <Pine.OSF.3.95.1030811004602.3417A-100000@plato.ucs.mun.ca>
References: <BAY7-F55f4aulqHFXfU0000d7f9@hotmail.com>
Message-ID: <5.1.0.14.2.20030811132603.02a463c0@mail1.monash.edu.au>

Derrick,

>i was just curious if anyone could answer a quick question, when i ran a
>simulation it produced two *.pdb file (step0.pdb and step-1.pdb) when i
>read the pdb file, the HEADER of step0.pdb stated "crash" and the HEADER
>of step-1.pdb stated "one step before crash". obviously this is cases a
>bit of concern on my part... so, could anyone fill me in to a possible
>cause for this crash? thank you.

Open them up and have a look.  In my experience, it tends to happen when 
the system is exploding for some reason, whether the entire system or some 
particular region.  Check your log files, that will have more complete 
details there on what is happening.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
--------------------------------------------------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
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From t.a.wassenaar at chem.rug.nl  Mon Aug 11 09:37:01 2003
From: t.a.wassenaar at chem.rug.nl (Tsjerk Wassenaar)
Date: Mon Aug 11 09:37:01 2003
Subject: [gmx-users] crash
References: <Pine.OSF.3.95.1030811004602.3417A-100000@plato.ucs.mun.ca>
Message-ID: <3F374685.4050504@chem.rug.nl>

Hi Derrick,

This doesn't say a thing about the nature of the crash. But considering 
that the first step already fails, there is probably something very 
wrong with your starting configuration. Have you energy minimized? Are 
there still any bad contacts, overlaps and so on?

Hope it helps. Cheers,

Tsjerk

Derrick Guang Yuh Lee wrote:

>dear gmx-users
>
>i was just curious if anyone could answer a quick question, when i ran a
>simulation it produced two *.pdb file (step0.pdb and step-1.pdb) when i
>read the pdb file, the HEADER of step0.pdb stated "crash" and the HEADER
>of step-1.pdb stated "one step before crash". obviously this is cases a
>bit of concern on my part... so, could anyone fill me in to a possible
>cause for this crash? thank you.
>
>
>sincerley
>
> - derrick
>
>
>
> derrick Lee
> faculty of Science
> Memorial University of Newfoundland
> k24dgyl at mun.ca or derrickglee at hotmail.com
> 
>"a teacher is never a giver of truth - he is a guide, a pointer to the
>truth that each student must find for himself. a good teacher is merely a
>catalyst." 
>                                                              - bruce lee
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~





From t.a.wassenaar at chem.rug.nl  Mon Aug 11 09:50:01 2003
From: t.a.wassenaar at chem.rug.nl (Tsjerk Wassenaar)
Date: Mon Aug 11 09:50:01 2003
Subject: [gmx-users] Error prb
References: <A1F8995C-CA55-11D7-853E-0050E41E2965@physbio.mssm.edu>
Message-ID: <3F374979.3020208@chem.rug.nl>

Dear Sachin,

Since the difference between your top file and the gro file is fourteen 
atoms, I would think it has to do with the adding of the ions. Seven 
waters would have been replaced by seven Cl-, giving a net change of 
fourteen atoms. So are you by chance using the old gro file, without the 
ions, with the modified topology file?

Cheers,

Tsjerk

Xavier Periole wrote:

>
> That is a simple one: the number of atoms defined in your topology
> file (topol.top) is different from the number of atoms that are your
> conf.gro. You have 14 atoms extra in the conf.gro that are not in the
> topology file. Check the missing atoms and include them in the
> topology file.
>
> XAvier
>
>
>
> On Saturday, August 9, 2003, at 02:30  pm, Sachin Gursahani wrote:
>
>> Dear friends....
>>
>> I ve this typical error while i was running the
>> simulation for Cytochrome C...
>>
>> Fatal error: number of coordinates in coordinate file
>> (1HRC_b4pr.gro, 10243)
>>              does not match topology (1HRC.top, 10229)
>> this error occured after i generated the pr.mdp
>> file..and while i was running:
>>
>> grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL}
>> -o ${MOL}_pr
>>
>> please anyone let me know how to solve this one ..
>> .
>> regards
>> Sachin
>>
>> note: ive used the command genion to genion to
>> generate 7 Cl ions coz the total charge on the system
>> is +7 and i wanted to make it 0....
>>
>> the nsteps for mdrun is 150000.
>>
>>
>>
>> __________________________________
>> Do you Yahoo!?
>> SBC Yahoo! DSL - Now only $29.95 per month!
>> http://sbc.yahoo.com
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~





From lpgomes at procc.fiocruz.br  Mon Aug 11 16:20:01 2003
From: lpgomes at procc.fiocruz.br (lpgomes at procc.fiocruz.br)
Date: Mon Aug 11 16:20:01 2003
Subject: [gmx-users] Hidrogen bond force
In-Reply-To: <20030811100001.7863.89456.Mailman@hawk.theophys.kth.se>
Message-ID: <20030811141416.19487F8251D@malaria.procc.fiocruz.br>

Hi All,

I would like to know how I could make hidrogen bond stronger.

Best regards,

Luciano P Gomes
FIOCRUZ/UnB


From mceruso at physbio.mssm.edu  Mon Aug 11 16:28:00 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Mon Aug 11 16:28:00 2003
Subject: [gmx-users] Hidrogen bond force
In-Reply-To: <20030811141416.19487F8251D@malaria.procc.fiocruz.br>
Message-ID: <IGEALMIPJBHPAJBIPPJEGEBGCAAA.mceruso@physbio.mssm.edu>

Hi-
The hydrogen bond interaction is not explicitly treated in gromacs, it
results from
both van der Waals and Coulombic interactions.
Marc


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of lpgomes at procc.fiocruz.br
Sent: Monday, August 11, 2003 10:18 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Hidrogen bond force


Hi All,

I would like to know how I could make hidrogen bond stronger.

Best regards,

Luciano P Gomes
FIOCRUZ/UnB
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.



From mceruso at physbio.mssm.edu  Mon Aug 11 16:28:01 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Mon Aug 11 16:28:01 2003
Subject: [gmx-users] Error prb
In-Reply-To: <3F374979.3020208@chem.rug.nl>
Message-ID: <IGEALMIPJBHPAJBIPPJEIEBGCAAA.mceruso@physbio.mssm.edu>

Hi
add #inlcude "ions.itp"
right after the DPOSRES_WATER stuff
to your topol.top
then delete 7 waters from the SOL line at end of .top
and then add a line at end of .top wiht the name of your ion and how many.
Marc

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Tsjerk Wassenaar
Sent: Monday, August 11, 2003 3:45 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Error prb



Dear Sachin,

Since the difference between your top file and the gro file is fourteen 
atoms, I would think it has to do with the adding of the ions. Seven 
waters would have been replaced by seven Cl-, giving a net change of 
fourteen atoms. So are you by chance using the old gro file, without the 
ions, with the modified topology file?

Cheers,

Tsjerk

Xavier Periole wrote:

>
> That is a simple one: the number of atoms defined in your topology
> file (topol.top) is different from the number of atoms that are your
> conf.gro. You have 14 atoms extra in the conf.gro that are not in the
> topology file. Check the missing atoms and include them in the
> topology file.
>
> XAvier
>
>
>
> On Saturday, August 9, 2003, at 02:30  pm, Sachin Gursahani wrote:
>
>> Dear friends....
>>
>> I ve this typical error while i was running the
>> simulation for Cytochrome C...
>>
>> Fatal error: number of coordinates in coordinate file
>> (1HRC_b4pr.gro, 10243)
>>              does not match topology (1HRC.top, 10229)
>> this error occured after i generated the pr.mdp
>> file..and while i was running:
>>
>> grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL}
>> -o ${MOL}_pr
>>
>> please anyone let me know how to solve this one ..
>> .
>> regards
>> Sachin
>>
>> note: ive used the command genion to genion to
>> generate 7 Cl ions coz the total charge on the system
>> is +7 and i wanted to make it 0....
>>
>> the nsteps for mdrun is 150000.
>>
>>
>>
>> __________________________________
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>> http://sbc.yahoo.com
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>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>> www interface or send it to gmx-users-request at gromacs.org.
>>
>
> _______________________________________________
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> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.



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From ysun at mie.utoronto.ca  Mon Aug 11 18:45:01 2003
From: ysun at mie.utoronto.ca (ysun at mie.utoronto.ca)
Date: Mon Aug 11 18:45:01 2003
Subject: [gmx-users] pull code for speptide
Message-ID: <1060620254.3f37c7dee731a@webmail.mie.utoronto.ca>

Dear GMX-users,

 Since no reply to my previous question, I want to seek your help again. 

 I am trying a pull code on example: speptide (under tutor/speptide).
 I applied pulling on a top atom (atom 9) and freeze at a bottom atom (atom
 140),
 
 and used 
 
 grompp -f pr.mdp -o prpull3 -c after_em -p speptide -n index.ndx
 
 mdrun -s prpull3.tpr -o prpull3 -c prpull3.gro -e prpull3.edr -g prpull3.log
 -
 pi pull.ppa -pn index.ndx
 
 The error came out:  "floating exception"
 
 Would appreciate if you could help me to identify the problem.
 
 I attached relevant files here for your information.
 
 Thanks in advance!
 
 Sun


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From mceruso at physbio.mssm.edu  Mon Aug 11 18:59:01 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Mon Aug 11 18:59:01 2003
Subject: [gmx-users] pull code for speptide
In-Reply-To: <1060620254.3f37c7dee731a@webmail.mie.utoronto.ca>
Message-ID: <IGEALMIPJBHPAJBIPPJEEEBHCAAA.mceruso@physbio.mssm.edu>

Hi,
AFAIK the pull code is not meant to "stretch" a molecule but to pull a
molecule/ion away/towards another molecule
Marc


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of ysun at mie.utoronto.ca
Sent: Monday, August 11, 2003 12:44 PM
To: gmx-users at gromacs.org
Cc: ysun at mie.utoronto.ca
Subject: Re: [gmx-users] pull code for speptide


Dear GMX-users,

 Since no reply to my previous question, I want to seek your help again.

 I am trying a pull code on example: speptide (under tutor/speptide).
 I applied pulling on a top atom (atom 9) and freeze at a bottom atom (atom
 140),

 and used

 grompp -f pr.mdp -o prpull3 -c after_em -p speptide -n index.ndx

 mdrun -s prpull3.tpr -o prpull3 -c prpull3.gro -e prpull3.edr -g
prpull3.log
 -
 pi pull.ppa -pn index.ndx

 The error came out:  "floating exception"

 Would appreciate if you could help me to identify the problem.

 I attached relevant files here for your information.

 Thanks in advance!

 Sun





From DaJustice1 at aol.com  Mon Aug 11 21:09:00 2003
From: DaJustice1 at aol.com (DaJustice1 at aol.com)
Date: Mon Aug 11 21:09:00 2003
Subject: [gmx-users] Amber OPLS dihedral conversion to GROMACS RB
Message-ID: <9b.3c95c57f.2c694394@aol.com>

Malcolm,

Thank you very much!   That is what I was thinking, but I wanted some 
clarification before jumping in head first.

David
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From ysun at mie.utoronto.ca  Mon Aug 11 22:23:01 2003
From: ysun at mie.utoronto.ca (ysun at mie.utoronto.ca)
Date: Mon Aug 11 22:23:01 2003
Subject: [gmx-users] pull code for speptide
Message-ID: <1060633321.3f37fae9dafa5@webmail.mie.utoronto.ca>

Thanks to Marc,

I am not sure if Gromacs could stretch on a group of molecules?
  
I WOULD appreciate if you could advise me more detail and suggest how to modify 
my pull code.

Thanks again.

Sun  


Quoting Marco Ceruso <mceruso at physbio.mssm.edu>:

> 
> Hi,
> AFAIK the pull code is not meant to "stretch" a molecule but to pull a
> molecule/ion away/towards another molecule
> Marc
> 
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of ysun at mie.utoronto.ca
> Sent: Monday, August 11, 2003 12:44 PM
> To: gmx-users at gromacs.org
> Cc: ysun at mie.utoronto.ca
> Subject: Re: [gmx-users] pull code for speptide
> 
> 
> Dear GMX-users,
> 
>  Since no reply to my previous question, I want to seek your help again.
> 
>  I am trying a pull code on example: speptide (under tutor/speptide).
>  I applied pulling on a top atom (atom 9) and freeze at a bottom atom (atom
>  140),
> 
>  and used
> 
>  grompp -f pr.mdp -o prpull3 -c after_em -p speptide -n index.ndx
> 
>  mdrun -s prpull3.tpr -o prpull3 -c prpull3.gro -e prpull3.edr -g
> prpull3.log
>  -
>  pi pull.ppa -pn index.ndx
> 
>  The error came out:  "floating exception"
> 
>  Would appreciate if you could help me to identify the problem.
> 
>  I attached relevant files here for your information.
> 
>  Thanks in advance!
> 
>  Sun
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 




From fmeyer at ix.urz.uni-heidelberg.de  Tue Aug 12 04:40:01 2003
From: fmeyer at ix.urz.uni-heidelberg.de (Frauke Meyer)
Date: Tue Aug 12 04:40:01 2003
Subject: [gmx-users] pull code for speptide
In-Reply-To: <1060633321.3f37fae9dafa5@webmail.mie.utoronto.ca>
Message-ID: <Pine.A41.4.42.0308120403200.28964-100000@aixterm3.urz.uni-heidelberg.de>

On Mon, 11 Aug 2003 ysun at mie.utoronto.ca wrote:

> Thanks to Marc,
>
> I am not sure if Gromacs could stretch on a group of molecules?
Well, I *am* using the pull code to pull the termini of a protein away
from each other - you can use it for this purpose I would say.

>
> I WOULD appreciate if you could advise me more detail and suggest how to modify
> my pull code.
> >  mdrun -s prpull3.tpr -o prpull3 -c prpull3.gro -e prpull3.edr -g
> > prpull3.log
> >  -
> >  pi pull.ppa -pn index.ndx
> >
> >  The error came out:  "floating exception"
> >
On what machine are you running it (which os)? Does the job run on another
one
without problems? Does it occur right before the first step, and is it due
to the pull code (just skip -pn and -pi and see what happens)?
I had that problem on a Dec Alpha cluster with OSF as operating system.
As for step=0 the force equals zero, one of the functions (increment of a
vector) caused the error, but this seems to very much depend on the
floating number/error handling.

Cheers,
Frauke

--
Frauke Meyer
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
Shanghai 201203
Tel: +86 21 50806600*1201, Fax: +86 21 50806600*1205
http://www.dddc.ac.cn, e-mail:frauke.meyer at mpi-bpc.mpg.de




From feenstra at chem.vu.nl  Tue Aug 12 09:01:02 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:01:02 2003
Subject: [gmx-users] equilibration
In-Reply-To: <Pine.SGI.3.96.1030808090333.24858M-100000@gretchen.fmp-berlin.de>
References: <Pine.SGI.3.96.1030808090333.24858M-100000@gretchen.fmp-berlin.de>
Message-ID: <3F33CA69.40602@chem.vu.nl>

Arvid Soederhaell wrote:
> Hi all
> I am trying to equilibrate a membrane-peptide-water-ion system but it
> doesn't work. Gromacs is quite new to me so the questions might be stupid.
> The system should already be quite well equilibrated since it comes from
> dynamics run using amber. The only thing that is done is making a new
> periodic box and adding hydrogens. 
> 
> I have tested to do a steepest descen minimization and the error message
> in the .log file is:  
> --------------------------------------------------------------------
> Stepsize too small (6.10352e-07 nm)Converged to machine precision, 
> but not to the requested precision (1) 

When the energy doesn't go down in an EM step, Gromacs decreases the step
size (i.e. the amount by which the atoms are moved along the energy gradient).
At some point, you drop below the arithmetic precision of the calculation,
i.e. the stepsize is so small that the coordinates do not change at all any
more. This is detected and the EM stops. This means that, although forces
are still high (higher than you set as convergence criterium), energy won't
go down. You're in a local minimum.

> You might need to increase your constraint accuracy, or turn off
> constraints alltogether (set constraints = none in mdp file) 
> 
> Steepest Descents did not converge in 15 steps
>   Potential Energy = nan Maximum force:  1.45952e+10

There is something defenitly not right with your coordinates, to
produce 'nan' energy, and a maximum force of 1e10! (For comparison,
I can generally minimize to maximum forces around 1e3.)

What do you mean by only 'making a new periodic box'? Did you re-solvate
your protein/bilayer? Did you 'trim' your system (i.e. removed a slice at
the edges) to get a smaller bilayer sheet and/or water box? Did you maybe
only edit the box size, without touching the atoms or coordinates?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|





From feenstra at chem.vu.nl  Tue Aug 12 09:01:03 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:01:03 2003
Subject: [gmx-users] equilibration
In-Reply-To: <003401c35dcd$821af730$d83a4a86@fox>
References: <Pine.SGI.3.96.1030808090333.24858M-100000@gretchen.fmp-berlin.de> <003401c35dcd$821af730$d83a4a86@fox>
Message-ID: <3F388523.8010708@chem.vu.nl>

Xavier Periole wrote:
>>A question that will be a problem later: I would like to scale the
>>temperature of the peptide, the lipids and water+ions separately. How
>>should I formulate this in the .mdp file? (How to put water and ions in
>>the same group?)
>>-------------------
>>tcoupl  = Berendsen
>>tc_grps = Protein DPPC (SOL Cl)   ?????
>>tau_t   =   0.1    0.1   0.1
>>ref_t   =    30     30    30
>>----------------------------
>>
> 
> 
> sounds good.

But isn't. You can't use brackets () in your .mdp file. You should create
a combined SOL+Cl index group first, using e.g. make_ndx (or a text editor).
Then, your .mdp file line would read:
tc_grps = Protein DPPC SOL+Cl

Where 'SOL+Cl' is the name of your combined Solvent and ions group, obviously.

> 
> 
>>The topology file looks like this (Note that in the [molecules] section
>>I have commented away the "Protein 1" line. If I keep thath line, grompp
>>complains and count the number of atoms in the protein twice!!?? The
>>rw-conn.itp file describes the peptide.):
[...]
>>[ molecules ]
>>; name number
>>;Protein 1
>>DPPC 64
>>SOL 2463
>>Cl 3
>>
> 
> Looks like there is a problem in the definition of your system. In your pdb
> or gro file is the order of appeareance protein, dppc, sol and CL ? That
> could be a conflict.

Is there already a [system]+[molecules] section in your rw-conn.itp? You
probably should remove that, and keep the line 'Protein 1' in your .top
file, to avoid confusion here. An .itp file for a molecule (peptide, protein,
lipid, whatever), should normally only contain [atoms], [bonds], [pairs],
[angles], [dihedrals] and [exclusions].


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Tue Aug 12 09:02:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:02:01 2003
Subject: [gmx-users] Topology File
In-Reply-To: <20030810212500.45740.qmail@web21501.mail.yahoo.com>
References: <20030810212500.45740.qmail@web21501.mail.yahoo.com>
Message-ID: <3F3888C0.8070101@chem.vu.nl>

Albert Sun wrote:
> Dear Users,
> 
> I wrote my own  .top  file and  ran the  em.mdp, here are errors 
> 
> WARNING 1 [file "try1.top", line 18]:
>   Invalid directive atom
> WARNING 2 [file "try1.top", line 22]:
>   Too few parameters on line (source file toppush.c, line 673)
> WARNING 3 [file "try1.top", line 23]:
> 
> 
> could you advise me how to avoid the errors?  I  attached my .top here.

I'm sorry, but you will have to do that all by yourself. It's a lot of
work, I know from experience, but you will simply have to work through it.
Read the topology chapter in the manual. Look at a couple of existing
topology files (e.g. from pdb2gmx, ProDrg, directory $GMXDATA/share/top)
to see how it is  done. Read the error messages carefully.

If that still leaves you stuck, feel free to ask again on the list.
It would help to know what molecule you are working on...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Tue Aug 12 09:02:03 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:02:03 2003
Subject: [gmx-users] [gmx-users]Running gromacs in parrallel environment.
In-Reply-To: <4d82584d39a4.4d39a44d8258@iit.edu>
References: <4d82584d39a4.4d39a44d8258@iit.edu>
Message-ID: <3F3885E5.7080607@chem.vu.nl>

Vishal Kumar Sinha wrote:
> Further , I want to run modify demo program so that
> I can run it on multiple nodes. Kindly let me know
> the changes needed to be made.

The demo program is only useful for demo. Do not use it for anything
else, I have seen several people getting terribly confused trying to
do that. If you want to test your parallel set-up, try one of the
benchmark systems. Try first on one CPU (you can compare the timings
with the web-pages), then on multiple.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Tue Aug 12 09:02:04 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:02:04 2003
Subject: [gmx-users] Error prb
In-Reply-To: <A1F8995C-CA55-11D7-853E-0050E41E2965@physbio.mssm.edu>
References: <A1F8995C-CA55-11D7-853E-0050E41E2965@physbio.mssm.edu>
Message-ID: <3F388925.40101@chem.vu.nl>

Xavier Periole wrote:
> 
> That is a simple one: the number of atoms defined in your topology
> file (topol.top) is different from the number of atoms that are your
> conf.gro. You have 14 atoms extra in the conf.gro that are not in the
> topology file. Check the missing atoms and include them in the
> topology file.

Yes, this is probably due to using genion. It has replacesd 7 waters with
7 Cl-, which leaves you 14 atoms short. Subtract 7 waters from the 'SOL'
line in your .top file, and add a line for 7 Cl-.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Tue Aug 12 09:02:05 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:02:05 2003
Subject: [gmx-users] infinite systems
In-Reply-To: <Pine.LNX.4.31.0308081940450.29914-100000@lisa.theochem.uni-frankfurt.de>
References: <Pine.LNX.4.31.0308081940450.29914-100000@lisa.theochem.uni-frankfurt.de>
Message-ID: <3F38876F.50308@chem.vu.nl>

Yuguang Mu wrote:
> Dear David,
> I want to simulate  an infinite system, a small peptide in water
> the system is quite small, total 200 atoms.
> if I use normal cut-off, the rcut  has to be smaller than box/2 (around 5
> A), then the simulated system is nonphysical, due to the small cutoff.
> I try to use setenv GMXFULLPBC 1, as:  export GMXFULLPBC=1, then use
> rcut=1nm .
> But the grompp still say it is a error : rcut > box/2.
> What should I do ?

Use a larger system. Since we do not have an 'infinite' long range method
for Van der Waals interactions (like PME does for Coulomb), you are stuck
with cut-offs. If you take your cut-off larger than half your box, you will
be counting interactions twice, and at some point atoms will interact with
their own periodic images. GMXFULLPBC doesn't change that, it only fixes
some assumptions that you cannot make if a molecule (e.g. a polymer)
stretches across the PBC (i.e., you have an infinite topology).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Tue Aug 12 09:02:07 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:02:07 2003
Subject: [gmx-users] A question on simulation carbon nanotubes
In-Reply-To: <MSG9V6P50NKyYCBklLX00005b3f@msg.sinr.ac.cn>
References: <MSG9V6P50NKyYCBklLX00005b3f@msg.sinr.ac.cn>
Message-ID: <3F388980.2010407@chem.vu.nl>

zhangwei wrote:
> Hi,everybody,
> 
>      I want to simulate carbon nanotubes with gromacs. Within the types of potentials given in Gromacs, I don't know how to construct the bonding interaction in the nanotubes. Could I simulate the bonds in a nanotube with only van de Waals potential? 

I don't know enough of the physics of nanotubes. To me they simply appear
like extended aromatics. Why would you not use simple harmonic bonds?


-- 
Groetjes,

Anton
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Tue Aug 12 09:02:08 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:02:08 2003
Subject: [gmx-users] Visualizing Gromacs trajectories with InsightII
In-Reply-To: <Pine.SGI.4.10.10308101640320.33431446-100000@cedar-f.csc.fi>
References: <Pine.SGI.4.10.10308101640320.33431446-100000@cedar-f.csc.fi>
Message-ID: <3F3889BA.8050105@chem.vu.nl>

Anu Tervo wrote:
> Dear all,
> 
> does anyone know how to visualize Gromacs trajectories with InsightII?
> When using Gromacs version 2.0, the thing goes something like:
> 
> trjconv -f trajectory.tpb -o trajectory.g87 -nog87box
> gtoarc1 system.gro trajectory.g87 trajectory.arc 
> 
> but it would be nice to visualize trajectories of newer gromacs versions
> as well (currently I'm using Gromacs 3.0.3 but it will be updated soon).
> It seems that gtoarc1 has been removed from version 3.0 -> so if someone
> knows any other way to generate Insight .arc file it would be nice to
> know!

gtoarc1 is not a gromacs tool.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Tue Aug 12 09:02:10 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 09:02:10 2003
Subject: [gmx-users] Hidrogen bond force
In-Reply-To: <IGEALMIPJBHPAJBIPPJEGEBGCAAA.mceruso@physbio.mssm.edu>
References: <IGEALMIPJBHPAJBIPPJEGEBGCAAA.mceruso@physbio.mssm.edu>
Message-ID: <3F388A06.70903@chem.vu.nl>

Marco Ceruso wrote:
> Hi-
> The hydrogen bond interaction is not explicitly treated in gromacs, it
> results from
> both van der Waals and Coulombic interactions.

Add a distance restraint, or a (harmonic) bond to the atoms concerned.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From sunita at chem.iitb.ac.in  Tue Aug 12 09:02:11 2003
From: sunita at chem.iitb.ac.in (Sunita Patel)
Date: Tue Aug 12 09:02:11 2003
Subject: [gmx-users] File not found error
Message-ID: <Pine.GSO.4.33.0308121224570.1285-100000@entropy.chem.iitb.ac.in>

Dear gmx-users,

I got 'file not found error' while trying to use 2.5 Gb .xtc file for
calculating g_dist. How Can I solve this problem?

Best wishes,
Sunita

-------------------------------------------------------------------------------
Sunita Patel
Biophysical Lab.,
Dept. of Chemistry,
Indian Institute of Technology(IIT) Bombay,
Powai, Mumbai, Maharashtra,
INDIA-400076.

Tel: (91)-22-25764176.
Email:sunita at chem.iitb.ac.in
-------------------------------------------------------------------------------





From mhuhtala at abo.fi  Tue Aug 12 09:38:01 2003
From: mhuhtala at abo.fi (Mikko Huhtala)
Date: Tue Aug 12 09:38:01 2003
Subject: [gmx-users] Re: Visualizing Gromacs trajectories with InsightII
In-Reply-To: <20030812070208.20795.74173.Mailman@hawk.theophys.kth.se>
References: <20030812070208.20795.74173.Mailman@hawk.theophys.kth.se>
Message-ID: <16184.39189.279330.364536@urquell.abo.fi>

 > Anu Tervo wrote:
 > > Dear all,
 > > 
 > > does anyone know how to visualize Gromacs trajectories with InsightII?
 > > When using Gromacs version 2.0, the thing goes something like:
 > 
 > gtoarc1 is not a gromacs tool.

gtoarc1, InsightII, the SGI hardware that runs it (and the
instructions at the CSC for doing all this) are all pretty much
obsolete. The combination runs so slowly at displaying large
trajectories that I'd say save your nerves. Unless you absolutely need
InsightII, skip it and use VMD on a reasonably powerful PC.

Mikko




From t.a.wassenaar at chem.rug.nl  Tue Aug 12 09:46:01 2003
From: t.a.wassenaar at chem.rug.nl (Tsjerk Wassenaar)
Date: Tue Aug 12 09:46:01 2003
Subject: [gmx-users] Error prb
References: <A1F8995C-CA55-11D7-853E-0050E41E2965@physbio.mssm.edu> <3F388925.40101@chem.vu.nl>
Message-ID: <3F389A0D.7030804@chem.rug.nl>

Pay attention Anton!

There are fourteen atoms *more* in the .gro file than in the .top file, 
not the other way around.

>> Fatal error: number of coordinates in coordinate file
>> (1HRC_b4pr.gro, 10243)
>>              does not match topology (1HRC.top, 10229)


Anton Feenstra wrote:

> Xavier Periole wrote:
>
>>
>> That is a simple one: the number of atoms defined in your topology
>> file (topol.top) is different from the number of atoms that are your
>> conf.gro. You have 14 atoms extra in the conf.gro that are not in the
>> topology file. Check the missing atoms and include them in the
>> topology file.
>
>
> Yes, this is probably due to using genion. It has replacesd 7 waters with
> 7 Cl-, which leaves you 14 atoms short. Subtract 7 waters from the 'SOL'
> line in your .top file, and add a line for 7 Cl-.
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~





From feenstra at chem.vu.nl  Tue Aug 12 11:12:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 11:12:01 2003
Subject: [gmx-users] File not found error
In-Reply-To: <Pine.GSO.4.33.0308121224570.1285-100000@entropy.chem.iitb.ac.in>
References: <Pine.GSO.4.33.0308121224570.1285-100000@entropy.chem.iitb.ac.in>
Message-ID: <3F38AFA9.6050502@chem.vu.nl>

Sunita Patel wrote:
> Dear gmx-users,
> 
> I got 'file not found error' while trying to use 2.5 Gb .xtc file for
> calculating g_dist. How Can I solve this problem?

Fix your OS, or maybe your Gromacs compile. Somewhere, 2Gb support is not enabled.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|



From feenstra at chem.vu.nl  Tue Aug 12 11:14:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 12 11:14:01 2003
Subject: [gmx-users] Error prb
In-Reply-To: <3F389A0D.7030804@chem.rug.nl>
References: <A1F8995C-CA55-11D7-853E-0050E41E2965@physbio.mssm.edu> <3F388925.40101@chem.vu.nl> <3F389A0D.7030804@chem.rug.nl>
Message-ID: <3F38B03B.8050308@chem.vu.nl>

Tsjerk Wassenaar wrote:
> 
> Pay attention Anton!
> 
> There are fourteen atoms *more* in the .gro file than in the .top file, 
> not the other way around.

Mea culpa. What a luck we have you around! ;-)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|



From oliver at biop.ox.ac.uk  Tue Aug 12 12:15:01 2003
From: oliver at biop.ox.ac.uk (Oliver Beckstein)
Date: Tue Aug 12 12:15:01 2003
Subject: [gmx-users] File not found error
In-Reply-To: <3F38AFA9.6050502@chem.vu.nl>
Message-ID: <Pine.LNX.4.44.0308121109230.13674-100000@choline.biop.ox.ac.uk>

On Tue, 12 Aug 2003, Anton Feenstra wrote:

> Sunita Patel wrote:
> > Dear gmx-users,
> >
> > I got 'file not found error' while trying to use 2.5 Gb .xtc file for
> > calculating g_dist. How Can I solve this problem?
> 
> Fix your OS, or maybe your Gromacs compile. Somewhere, 2Gb support is
> not enabled.

Not sure if it is a simple 'user error'. The last time I checked (2 months
ago),

http://www.gromacs.org/pipermail/gmx-users/2003-May/032227.html

the consensus seemed to be that it required adding the O_LARGEFILE flag to
open() calls in gromacs. (Have to admit that I didn't find the time to
tinker with the source myself, mainly because the workaround (accessing
files through nfs) works for me.)

Oliver

--
Oliver Beckstein * oliver at bioch.ox.ac.uk
 http://indigo1.biop.ox.ac.uk/oliver/



From k24dgyl at morgan.ucs.mun.ca  Tue Aug 12 20:06:01 2003
From: k24dgyl at morgan.ucs.mun.ca (Derrick Guang Yuh Lee)
Date: Tue Aug 12 20:06:01 2003
Subject: [gmx-users] 1 ps simulation
In-Reply-To: <3F374685.4050504@chem.rug.nl>
Message-ID: <Pine.OSF.3.95.1030812152222.31903A-100000@plato.ucs.mun.ca>

dear gmx-users

i was just curious, i am attempting to run a simulation for 1 ps and i
want it to spit out coordinates, velocities, etc every couple of ns. do i
need to adjust the mdp file or will it do it for me automatically?


 - derrick

 

 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com
 
"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst." 
                                                              - bruce lee



From mceruso at physbio.mssm.edu  Tue Aug 12 20:27:00 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Tue Aug 12 20:27:00 2003
Subject: [gmx-users] 1 ps simulation
In-Reply-To: <Pine.OSF.3.95.1030812152222.31903A-100000@plato.ucs.mun.ca>
Message-ID: <IGEALMIPJBHPAJBIPPJEGEBLCAAA.mceruso@physbio.mssm.edu>


dear gmx-users

i was just curious, i am attempting to run a simulation for 1 ps and i
want it to spit out coordinates, velocities, etc every couple of ns.
>> Did you mean the other way around ? 1ns MD and write every couple of ps?


do i need to adjust the mdp file or will it do it for me automatically?

>>In any case you need to adjust  dt,
nsteps,nstxtcout,nstxout,nstvout,nstfout,nstenergy in the .mdp as per your
needs

Marc

 - derrick



 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com

"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst."
                                                              - bruce lee

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.



From osmany.guirola at cigb.edu.cu  Tue Aug 12 21:42:01 2003
From: osmany.guirola at cigb.edu.cu (Osmany Guirola Cruz)
Date: Tue Aug 12 21:42:01 2003
Subject: [gmx-users] pH
Message-ID: <E78E51BB7B45C749B11C8B5BA64107E105C45C68@mercurio.cigb.edu.cu>

 Hi 
Two questions.I have my system(for example a peptide in a box of water)
How can I calculate the pH of the sysytem and 
How can I do a simulation of this system whith a given pH.
For example I want a simulation of the system whith pH=4 and another
whith
pH=9..  
Thanks...

                 



From oliver at biop.ox.ac.uk  Tue Aug 12 22:02:01 2003
From: oliver at biop.ox.ac.uk (Oliver Beckstein)
Date: Tue Aug 12 22:02:01 2003
Subject: [gmx-users] pH
In-Reply-To: <E78E51BB7B45C749B11C8B5BA64107E105C45C68@mercurio.cigb.edu.cu>
Message-ID: <Pine.LNX.4.44.0308122045560.19918-100000@choline.biop.ox.ac.uk>

Hi,

I think you wouldn't typically put xN protons and 10^-14/x N OH- in your
simulation box; if you do the math you'll see that with a N = few thousand
water molecules in your simulation you won't get many protons at
these pH... 

So what people do is calculate the protonation states of the titrable
sidechains in a static structure at a given pH and use these as input
for their MD simulations. In order to obtain titration curves the free
energy of ionisation of a sidechain has to be calculated. These are
electro static calculations in presence of a salt solution. Typically,
this means that the (linearised) Poisson-Boltzmann equation has to be
solved repeatedly, using your choice of DelPhi, UHB, APBS, ...

However, Jose Faraldo-G?mez, a colleague of mine, has written half a
thesis about this, which is online available at
http://sansom.biop.ox.ac.uk/josed/home.html (see especially Chapter
4). This uses UHBD and a couple of home grown scripts.

Alternatively you can look at WhatIf/DelPhi, and here I can recommend
Jens Nielsen's pages,
http://mccammon.ucsd.edu/~jnielsen/manuals/pKa.html and links from
http://mccammon.ucsd.edu/~jnielsen/

HTH,
Oliver

On Tue, 12 Aug 2003, Osmany Guirola Cruz wrote:

>  Hi 
> Two questions.I have my system(for example a peptide in a box of water)
> How can I calculate the pH of the sysytem and 
> How can I do a simulation of this system whith a given pH.
> For example I want a simulation of the system whith pH=4 and another
> whith
> pH=9..  
> Thanks...


-- 
Oliver Beckstein * oliver at bioch.ox.ac.uk
 http://indigo1.biop.ox.ac.uk/oliver/



From mceruso at physbio.mssm.edu  Tue Aug 12 22:12:01 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Tue Aug 12 22:12:01 2003
Subject: [gmx-users] pH
In-Reply-To: <E78E51BB7B45C749B11C8B5BA64107E105C45C68@mercurio.cigb.edu.cu>
Message-ID: <IGEALMIPJBHPAJBIPPJEOEBLCAAA.mceruso@physbio.mssm.edu>

Hi
check out this webpage:
http://fulcrum.physbio.mssm.edu/~mehler/
there is a link to a method that predict pKa values of aa in proteins. There
are other methods, as well. There was a discussion about some of them in the
list a few months ago.
In any case once you have determined the pKa of your titrable groups you
will assign the corresponding protonation state accordingly.
If you don't want to run a pKa calculation some standard values of pKa are
given in biochemistry text books, but you should be aware that e.g. the pKa
of buried titratble aa may deviate significantly from these standards
Marc

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Osmany Guirola Cruz
Sent: Tuesday, August 12, 2003 3:41 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] pH


 Hi
Two questions.I have my system(for example a peptide in a box of water)
How can I calculate the pH of the sysytem and
How can I do a simulation of this system whith a given pH.
For example I want a simulation of the system whith pH=4 and another
whith
pH=9..
Thanks...



_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.



From ysun at mie.utoronto.ca  Tue Aug 12 22:40:01 2003
From: ysun at mie.utoronto.ca (Yabias Sun)
Date: Tue Aug 12 22:40:01 2003
Subject: [gmx-users] pull code for speptide : floating exception
Message-ID: <200308122039.QAA19362@mie.utoronto.ca>

Hi, Frauke, 
Thank you very much for your reply.

As you advised. I tried to skip -pn -pi, it worked and got output results.
However, when added -pn -pi in the mdrun, it had error: "floating exception" 
just occurred at the beginning (may be the first step)!

YOU mentioned you met this problem, due to step=0 the force equal zero, one of 
the function caused the error, how did you solve your problem at that time?

Thank you and best regards,

sun 
 	



From k24dgyl at morgan.ucs.mun.ca  Tue Aug 12 22:50:01 2003
From: k24dgyl at morgan.ucs.mun.ca (Derrick Guang Yuh Lee)
Date: Tue Aug 12 22:50:01 2003
Subject: [gmx-users] 1 ps simulation
In-Reply-To: <IGEALMIPJBHPAJBIPPJEGEBLCAAA.mceruso@physbio.mssm.edu>
Message-ID: <Pine.OSF.3.95.1030812181857.14250C-100000@plato.ucs.mun.ca>

dear marc

yes, i meant it the other way around, and thanks for the info.


sincerely

 - derrick



 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com
 
"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst." 
                                                              - bruce lee

On Tue, 12 Aug 2003, Marco Ceruso wrote:

> 
> 
> dear gmx-users
> 
> i was just curious, i am attempting to run a simulation for 1 ps and i
> want it to spit out coordinates, velocities, etc every couple of ns.
> >> Did you mean the other way around ? 1ns MD and write every couple of ps?
> 
> 
> do i need to adjust the mdp file or will it do it for me automatically?
> 
> >>In any case you need to adjust  dt,
> nsteps,nstxtcout,nstxout,nstvout,nstfout,nstenergy in the .mdp as per your
> needs
> 
> Marc
> 
>  - derrick
> 
> 
> 
>  derrick Lee
>  faculty of Science
>  Memorial University of Newfoundland
>  k24dgyl at mun.ca or derrickglee at hotmail.com
> 
> "a teacher is never a giver of truth - he is a guide, a pointer to the
> truth that each student must find for himself. a good teacher is merely a
> catalyst."
>                                                               - bruce lee
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 



From periole at inka.mssm.edu  Tue Aug 12 22:59:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Tue Aug 12 22:59:01 2003
Subject: [gmx-users] pH
References: <E78E51BB7B45C749B11C8B5BA64107E105C45C68@mercurio.cigb.edu.cu>
Message-ID: <007301c36114$69bc63a0$d83a4a86@fox>

The pH involves the entities OH- and H+(H3O+). Do you have any in
your system ? Probably not !! They do not exist in any Molecular 
Dynamics force field I know. I don't know any way to do explicit 
solvent simulations with a control of pH. 
I assume that the pH can be introduce when the solvent is introduced 
explicitly. But I don't know either any explicit solvent where you can 
actually modify your pH. Does any one ??? 

XAvier




From periole at inka.mssm.edu  Tue Aug 12 23:01:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Tue Aug 12 23:01:01 2003
Subject: [gmx-users] pH
References: <E78E51BB7B45C749B11C8B5BA64107E105C45C68@mercurio.cigb.edu.cu>
Message-ID: <008801c36114$c05baea0$d83a4a86@fox>

You can take a look at this paper :

http://www.igc.ethz.ch/phil/pdf/01.18.pdf


XAvier




From F.Hao at chem.rug.nl  Tue Aug 12 23:05:01 2003
From: F.Hao at chem.rug.nl (F.Hao at chem.rug.nl)
Date: Tue Aug 12 23:05:01 2003
Subject: [gmx-users] position restrain energy in stochastic dynamics
Message-ID: <Pine.LNX.4.33.0308122245460.14634-100000@rugmd7.chem.rug.nl>

Hi, all:
	I want to run prosition restrained sd with a protein molecule.
What I did is:
	grompp -f prsd.mdp -c em.gro -r em.gro -p protein.top -o topol.tpr
In the prsd.mdp, I used "define = -DPOSRE". So I think I should have
included the posre.itp file. But I could not find related information
in topol.tpr file by gmxdump. If I use this topol.tpr for mdrun, there was
no position restrain energy term output with g_energy. Does this mean I
have done anything wrong or the energy term of position restrain is
built-in with others? Thanks a lot in advance!

Best regards

Yours sincerely

Hao Fan :-)

-------------------------------------------------------------------------
Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands
-------------------------------------------------------------------------



From periole at inka.mssm.edu  Tue Aug 12 23:33:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Tue Aug 12 23:33:01 2003
Subject: [gmx-users] position restrain energy in stochastic dynamics
References: <Pine.LNX.4.33.0308122245460.14634-100000@rugmd7.chem.rug.nl>
Message-ID: <00a901c36119$2f768900$d83a4a86@fox>

]> In the prsd.mdp, I used "define = -DPOSRE". So I think I should have
>

I think it is -DPOSRES and not -DPOSRE. Could it be the reason ??


XAvier
 



From PNAGY at UTNet.UToledo.Edu  Wed Aug 13 00:26:01 2003
From: PNAGY at UTNet.UToledo.Edu (Nagy, Peter I.)
Date: Wed Aug 13 00:26:01 2003
Subject: [gmx-users] palmitoyl
Message-ID: <B16CE043598D02408DC7DE5A36B2767C0AA5B7@msgdb01.utad.utoledo.edu>

Dear Gromacs Users!

   I have a CYS residue with a palmitoyl group on that, replacing the thiol hydrogen. When I downloaded the hydrated membrane bilayer model, GROMACS understood the DPP code of the.pdb file as DPPC. This molecule contains both
regular and phophate-ester groups, but it was an independent unit. What will 
GROMACS do with a thiol ester on CYS, and how would the program handle the aliphatic chain?
   I assume that I will have to modify some parameter files and adding MD parameters for the C-S-C(=O)-C-C subunit. Please give me some clues where and how to start.

   Thanks, Peter Nagy
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From periole at inka.mssm.edu  Wed Aug 13 00:46:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Wed Aug 13 00:46:01 2003
Subject: [gmx-users] palmitoyl
References: <B16CE043598D02408DC7DE5A36B2767C0AA5B7@msgdb01.utad.utoledo.edu>
Message-ID: <00d101c36123$5c7be940$d83a4a86@fox>

palmitoyl
For the DPP/DPPC problem you just have to modifu the name in the pdb
file. Substitution within a vi session. Becarefull to modify "DPP_" and not only
"DPP". The number of caracters is important. 

For the CYS, you have to define a  new residue CYS with the extra part 
(palmitoyl). Using existing parameters, the charges by ab initio or existing
calculations

XAvier
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From baaden at smplinux.de  Wed Aug 13 09:30:01 2003
From: baaden at smplinux.de (Marc Baaden)
Date: Wed Aug 13 09:30:01 2003
Subject: [gmx-users] pH 
In-Reply-To: Your message of "Tue, 12 Aug 2003 16:57:59 EDT."
             <007301c36114$69bc63a0$d83a4a86@fox> 
Message-ID: <200308130729.JAA07961@apex.ibpc.fr>

Hi,

we did some work on the influence of acidity. Unfortunately it does
not go as far as using a real pH, but we rather did test extreme cases
where you have explicit acid molecules present which are either
dissociated, associated or partly dissociated by protonating part
of the system.
In our case it did make sense because the real concentrations in
the system we were looking at (nuclear waste recycling) were *very*
acidic.
But one can always try it.

If you are interested, have a look at

     M. Baaden, F. Berny and G. Wipff; "The chloroform / TBP / aqueous
     nitric acid interfacial system: a molecular dynamics
     investigation.", J. Mol. Liq., 90, 2001, 1-9.

     M. Baaden, M. Burgard, and G. Wipff; "TBP at the water - oil
     interface: the effect of TBP concentration and water acidity
     investigated by molecular dynamics simulations", J. Phys. Chem.
     B, 105, 2001, 11131-11141


For a protein with ionizable sidechains it would however in any case
be necessary to do a pka calculation in addition and adapt the protonation
states.

Marc

>>> "Xavier Periole" said:
 >> 
 >> The pH involves the entities OH- and H+(H3O+). Do you have any in
 >> your system ? Probably not !! They do not exist in any Molecular 
 >> Dynamics force field I know. I don't know any way to do explicit 
 >> solvent simulations with a control of pH. 
 >> I assume that the pH can be introduce when the solvent is introduced 
 >> explicitly. But I don't know either any explicit solvent where you can 
 >> actually modify your pH. Does any one ??? 
 >> 
 >> XAvier
 >> 
 >> 
 >> _______________________________________________
 >> gmx-users mailing list
 >> gmx-users at gromacs.org
 >> http://www.gromacs.org/mailman/listinfo/gmx-users
 >> Please don't post (un)subscribe requests to the list. Use the 
 >> www interface or send it to gmx-users-request at gromacs.org.
 >> 

Marc Baaden

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217




From ygmu at theochem.uni-frankfurt.de  Wed Aug 13 14:39:00 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Wed Aug 13 14:39:00 2003
Subject: [gmx-users] secondary structure
In-Reply-To: <1059644932.27733.17.camel@werkman.bmc.uu.se>
Message-ID: <Pine.LNX.4.44.0308131437140.3035-100000@marge.theochem.uni-frankfurt.de>

Dear All,
DO you have some good suggestions about the programs to assign
the secondary structures of peptides, proteins with known coordinates,
such as, alpha, beta, turns, 3_10 helix ?


Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711




From ikass at cc.huji.ac.il  Wed Aug 13 14:46:02 2003
From: ikass at cc.huji.ac.il (Itamar Kass)
Date: Wed Aug 13 14:46:02 2003
Subject: [gmx-users] secondary structure
References: <Pine.LNX.4.44.0308131437140.3035-100000@marge.theochem.uni-frankfurt.de>
Message-ID: <000c01c361a1$6e05f920$7b414084@tmpc1>

   You can use Sybyl or InsightII.


----- Original Message ----- 
From: "Yuguang Mu" <ygmu at theochem.uni-frankfurt.de>
To: <gmx-users at gromacs.org>
Sent: Wednesday, August 13, 2003 2:37 PM
Subject: [gmx-users] secondary structure


> 
> Dear All,
> DO you have some good suggestions about the programs to assign
> the secondary structures of peptides, proteins with known coordinates,
> such as, alpha, beta, turns, 3_10 helix ?
> 
> 
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 


From mceruso at physbio.mssm.edu  Wed Aug 13 16:26:02 2003
From: mceruso at physbio.mssm.edu (Marc Ceruso)
Date: Wed Aug 13 16:26:02 2003
Subject: [gmx-users] secondary structure
In-Reply-To: <Pine.LNX.4.44.0308131437140.3035-100000@marge.theochem.uni-frankfurt.de>
Message-ID: <Pine.SGI.4.44.0308131022320.5066756-100000@fulcrum.physbio.mssm.edu>


On Wed, 13 Aug 2003, Yuguang Mu wrote:

>
> Dear All,
> DO you have some good suggestions about the programs to assign
> the secondary structures of peptides, proteins with known coordinates,
> such as, alpha, beta, turns, 3_10 helix ?
>
if you have the coordinates of your peptide, you can try stride or dssp...
if you need to build your peptide with a certain secondary structure you
can try swiss pdbviewer/Deepview.





>
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From PNAGY at UTNet.UToledo.Edu  Wed Aug 13 18:15:01 2003
From: PNAGY at UTNet.UToledo.Edu (Nagy, Peter I.)
Date: Wed Aug 13 18:15:01 2003
Subject: [gmx-users] parameters/references
Message-ID: <B16CE043598D02408DC7DE5A36B2767C0AA5B9@msgdb01.utad.utoledo.edu>

Dear GROMACS Users!

   I will have to estimate parameters for a non-standard side chain and for different ligands. I checked the section Force Fields in the 3.1 manual, and found reference 39, which is another manual. Could somebody give me one or more journal references where the parameter estimation for GROMACS/GROMOS96 is described. I mean the ab initio level for obtaining charges, equilibrium bond lengths and bond angles. I read from the manual that the force constant may be estimated from the harmonic approximation. So I would like to know what level
(semiempirical, HF, B3LYP, MP2,...) and basis set was used for calculating the abovementioned parameters.

Thank, Peter Nagy
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From baptista at itqb.unl.pt  Wed Aug 13 20:29:01 2003
From: baptista at itqb.unl.pt (baptista at itqb.unl.pt)
Date: Wed Aug 13 20:29:01 2003
Subject: [gmx-users] pH
In-Reply-To: <E78E51BB7B45C749B11C8B5BA64107E105C45C68@mercurio.cigb.edu.cu>
Message-ID: <Pine.LNX.4.33.0308131430100.11068-100000@medusa.itqb.unl.pt>

Dear Osmany,

>  Hi
> Two questions.I have my system(for example a peptide in a box of water)
> How can I calculate the pH of the sysytem and

First of all, I sincerely doubt that you really want to *compute* the pH.
The reason can be made more clear if I make a parallel with a more
familiar property, the temperature. (I'll ignore volume/pressure stuff in
what follows.) The ideal way to perform a simulation of your solvated
peptide is to use a constant-temperature algorithm, which directly
reflects the heat-bath effect of the surrounding solution. Imagine,
though, that there were no constant-temperature algorithms around and all
you had was a plain constant-energy algorithm. Of course, you could
perform a constant-energy simulation and *compute* the energy afterward
(from the average kinetic energy), but the only reason to do so would be
to try finding out an energy value giving the temperature you wanted for
your system: with it you could then make the simulation at the intended
temperature (note that, in practice, the energy value alone is useless:
eg, if you want to relate your simulations with experiments done in your
peptide at 300K, you have no idea what was the typical energy of a
"peptide+water box" in that experiment). But the constant-temperature
algorithm is the ideal way of performing the simulation, since you don't
need to waste time trying out different energy values. Furthermore, for
the small (non-macroscopic) systems used in simulations you have an
additional, extremely important reason for preferring a
constant-temperature algorithm: a constant-energy algorithm neglects
energy fluctuations that may be crucial for the system. The fluctuations
of all "mechanical" properties (phase functions) in a constant-temperature
system are larger than in a constant-energy one, which, eg, helps the
system to overcome local energy barriers, not to mention the entropic role
of fluctuations. Theoretically, this may be stated by saying that you
should use a proper ensemble when getting fluctuations. Thus, the natural
thermodynamic parameter for your system is the temperature, not the
energy, both from experimental and theoretical viewpoints. Thus, you want
to *impose* the temperature in your simulation, not *compute* it.

The situation concerning pH is identical. A pH-buffered solution works
both as a heat bath and as a H+ bath. Thus, the ideal situation would be
to have a constant-pH algorithm to perform the MD simulations. However,
conventional MD algorithms cannot do that, since they're constant-H+
algorithms. Furthermore, if you use a MM force field, you will never get
protonation/deprotonation of sites in your solute: free H+ will just
wander around, while titrable sites are stuck with their initial
protonation states; if you want to overcome this you have to use a non-MM
Hamiltonian which explicitly allows for proton transfer. In any case,
regardless of the Hamiltonian used, the amount of H+ would never change.
Of course, for a given amount of H+, you may wander to which pH value this
corresponds and even try to *compute* it (eg, using some variant of
Widom's particle insertion method), but, as in the energy/temperature
case, that is not the interesting thing to do. The interesting thing would
be to devise a proper algorithm for constant-pH MD and then *impose* the
intended pH value in your simulation. Which lead to your second
question...

> How can I do a simulation of this system whith a given pH.
> For example I want a simulation of the system whith pH=4 and another
> whith
> pH=9..

The simplest thing to do is to stick to conventional MD and just select
the particular amount of H+ that is "typical" for your system. As noted in
other replies, you can neglect free H+: at most pH values (even at pH=4)
its concentration is orders of magnitude below that of other counterions
(eg, Na+, Cl-). Furthermore, as noted above, a pure MM Hamiltonian will be
unable to move protons between titrable sites (eg, unlike EVB), so you
actually need to select a particular configuration of protonation states,
ie, you need to choose the protonation state of each titrable site in your
molecule. As also noted in some of the previous replies, you can get a
good guess by performing a standard pKa calculation with your starting
structure; these are standard procedures, mostly based on continuum
electrostatics for computing protonation free energies (eg, using MEAD,
UHBD, DELPHI, APBS) and Monte Carlo to perform sampling of protonation
states (eg, using REDTI, PETIT). Unfortunately, as the conformation of the
solute changes along the MD simulation, the protonation states may become
inadequate, due to the strong protonation-conformation coupling that
exists in many cases. Several solutions have been proposed (including by
myself), but most of them are more or less heuristic attempts. The truly
satisfactory solution would be to have a constant-pH MD method, and some
have been proposed in the last years. I have discussed that issue recently
in this list, so please have a look at
http://www.gromacs.org/pipermail/gmx-users/2003-April/031920.html. (Note
that there is a serious theoretical problem with a method by Phil
Hunenberger, whose paper was linked to by a previous reply; see my
previous message.) Unfortunately, constant-pH methods are recent and still
under development and/or testing. Hopefully, they will become standard
methods in the near future. Maybe you could one of these days just specify
"pH = 7.0" in the GROMACS .mdp file and see protonation states changing
during the MD run! :-) Until then, the best solution is probably to one
mentioned above: make an initial good guess with a standard pKa
calculation, and eventually check it later with snapshots from the MD run.

> Thanks...
>

Regards,
Antonio

-- 
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica, EAN, ITQB II, Piso 6, Apartado 127
2781-901 Oeiras, Portugal
phone: +351-214469619(NEW!)   email: baptista at itqb.unl.pt
fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/~baptista
--------------------------------------------------------------------------



From vraut at CLEMSON.EDU  Wed Aug 13 21:19:01 2003
From: vraut at CLEMSON.EDU (Vivek Raut)
Date: Wed Aug 13 21:19:01 2003
Subject: [gmx-users] how to modify Dielectric constant (DC)
Message-ID: <5.1.1.5.2.20030813151407.00a70ee8@mail.clemson.edu>

Hi,

I need to change Dielectric constant (DC) (epsilon-r ) for my simulation. 
How to do it?... I dont find such a factor in  .mdp files, but that value 
is mentioned =1 in the mdout.mdp.

Can anyone help?

Vivek


-------------------------------------------------------------------------------------------------------------------------------------------
Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
--------------------------------------------------------------------------------------------------------------------------------------------



From lzheng at me.rochester.edu  Wed Aug 13 21:22:01 2003
From: lzheng at me.rochester.edu (Lianqing Zheng)
Date: Wed Aug 13 21:22:01 2003
Subject: [gmx-users] how to modify Dielectric constant (DC)
In-Reply-To: <5.1.1.5.2.20030813151407.00a70ee8@mail.clemson.edu>
Message-ID: <Pine.SOL.3.96.1030813152054.17518E-100000@isaac.me.rochester.edu>

add epsilon_r = xxx in .mdp


On Wed, 13 Aug 2003, Vivek Raut wrote:

>Hi,
>
>I need to change Dielectric constant (DC) (epsilon-r ) for my simulation. 
>How to do it?... I dont find such a factor in  .mdp files, but that value 
>is mentioned =1 in the mdout.mdp.
>
>Can anyone help?
>
>Vivek
>
>
>-------------------------------------------------------------------------------------------------------------------------------------------
>Vivek Raut
>Graduate Research Assistant
>Department of Bioengineering
>Clemson University
>Clemson, SC- 29631. USA
>Email: vraut at clemson.edu
>Phone: 864-650-1431
>--------------------------------------------------------------------------------------------------------------------------------------------
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>



From vraut at CLEMSON.EDU  Wed Aug 13 21:34:01 2003
From: vraut at CLEMSON.EDU (Vivek Raut)
Date: Wed Aug 13 21:34:01 2003
Subject: [gmx-users] how to modify Dielectric constant (DC)
In-Reply-To: <Pine.SOL.3.96.1030813152054.17518E-100000@isaac.me.rochest
 er.edu>
References: <5.1.1.5.2.20030813151407.00a70ee8@mail.clemson.edu>
Message-ID: <5.1.1.5.2.20030813153202.00a73940@mail.clemson.edu>

OK, but how to do that on only some specific part of the box?? ( say a 
section across y coordinate??)

At 03:21 PM 8/13/2003 -0400, you wrote:
>add epsilon_r = xxx in .mdp
>
>
>On Wed, 13 Aug 2003, Vivek Raut wrote:
>
> >Hi,
> >
> >I need to change Dielectric constant (DC) (epsilon-r ) for my simulation.
> >How to do it?... I dont find such a factor in  .mdp files, but that value
> >is mentioned =1 in the mdout.mdp.
> >
> >Can anyone help?
> >
> >Vivek
> >
> >
> >------------------------------------------------------------------------- 
> ------------------------------------------------------------------
> >Vivek Raut
> >Graduate Research Assistant
> >Department of Bioengineering
> >Clemson University
> >Clemson, SC- 29631. USA
> >Email: vraut at clemson.edu
> >Phone: 864-650-1431
> >------------------------------------------------------------------------- 
> -------------------------------------------------------------------
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.

-------------------------------------------------------------------------------------------------------------------------------------------
Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
--------------------------------------------------------------------------------------------------------------------------------------------



From aborics at bif12.creighton.edu  Wed Aug 13 22:05:01 2003
From: aborics at bif12.creighton.edu (Attila Borics)
Date: Wed Aug 13 22:05:01 2003
Subject: [gmx-users] (no subject)
Message-ID: <200308131820.h7DIKO229176@bif12.creighton.edu>

Hi,

I tried to use g_rms to analyze my trajectory, but I got really weird results.
g_rms -h says, that each structure from the trajectory is compared to a reference structure, wich is taken from the .tpr file. I ran g_rms on my trajectory, and I got very high RMSD values (0.5nm) even the first (starting) structure of my trajectory. I chopped out my starting structure from the trajectory and and calculated its RMSD compared to the .pdb file I used for input generation (pdb2gmx, and grompp) previously. The result was 0.0 in contrast with 0.5098, what g_rms yielded for the same structure (and what doesn't make any sense).
So there is a problem with g_rms, or I just did something wrong.
There's one little thing with the usage of g_rms, which is a bit fuzzy for me, so I try to describe what I did.

g_rms -s xxxxx.tpr -f xxxxx.xtc -n index.ndx -o rmsd

Select group for least squares fit

Group     4 (    Backbone) has   603 elements

How many groups do you want to compare ? 1
OK. I will compare 1 groups

Group     4 (    Backbone) has   603 elements


So as I believe I just fitted the backbone of each structure in my trajectory to the backbone of reference structure and calculated RMSD for each. Is that right?
Or I just misunderstood something?
Thanks in advance. 

Attila

From periole at inka.mssm.edu  Wed Aug 13 23:02:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Wed Aug 13 23:02:01 2003
Subject: [gmx-users] (no subject)
References: <200308131820.h7DIKO229176@bif12.creighton.edu>
Message-ID: <002201c361dd$fa2ce9e0$d83a4a86@fox>


I there any possibility that your .tpr has been modified after you began
your
simulation : simulation restarted for example
I would try to rebuild a .tpr with the original pdb file if I was you ! And
see !


XAvier




From ridgway at dridgway.com  Thu Aug 14 01:01:02 2003
From: ridgway at dridgway.com (Douglas Ridgway)
Date: Thu Aug 14 01:01:02 2003
Subject: [gmx-users] PRODRG and partial charges
Message-ID: <Pine.LNX.4.33.0308131149390.8254-100000@localhost>

I'm confused about how to assign partial charges. I did some browsing of 
the archives, so I know this has come up before, and have started to read 
some papers, but I'm still confused.

One suggestion is to use PRODRG, another is to get partial charges from
QM, and I've also read that QM charges are too big and should *not* be
used. PRODRG offers both "full" and "partial"  charges, though I'm not
sure what these mean exactly.

My interest is drug molecules in membranes. At the moment, though, I'm 
playing with octanol. Octanol has some charge at the end, due to the 
hydroxyl. The question is how much. Here's a table of some possible 
charges for the last carbon, the oxygen, and its attached hydrogen:


             C        O      H
partial    0.026  -0.091  0.013
full       0.043  -0.151  0.022
a          0.040  -0.060  0.020
G45a3      0.150  -0.548  0.398
G45a3MOD   0.156  -0.563  0.407
I2         0.117  -0.323  0.181

"partial" and "full" came from PRODRG today. "a" also came from PRODRG, 
but a couple weeks ago, and I can't seem to reproduce it. (My notes show 
I've gotten other results on full charges too. Perhaps I'm doing something 
different or wrong?) 

The lines G45 etc. come from McCallum and Tieleman, JACS 124 15085-. The 
G45a3 line is also the same as the example given in the PRODRG paper of a 
charge group. The line I2 was generated by a collegue using Insight II to 
run some quantum calculation in a way I don't entirely understand.

The spread in values looks fairly wide, with the PRODRG values much lower
than the McCallum paper, and the QM values inbetween. It also seems to be
significant: I've run short simulations of octanol and water using both
"a" and "G45a3MOD". The results are visually quite different: "a" looks
fairly disordered, while "G45a3MOD" octanols line up straight and
parallel, at an angle to the octanol water interface. ffgmx force field,
SPC water, PME, rvdw=1.2.

Do charges need to be parameterized with the rest of a force field?  Will
they depend on cutoffs, other molecules and such? How do you do this for a
new molecule? How arbitrary is it? And how do you figure out what results
to believe?

Sorry for all the questions! I'm still trying to get a clue about MD...

doug.



From lindahl at stanford.edu  Thu Aug 14 01:25:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Thu Aug 14 01:25:01 2003
Subject: [gmx-users] PRODRG and partial charges
In-Reply-To: <Pine.LNX.4.33.0308131149390.8254-100000@localhost>
Message-ID: <2D68ECA4-CDE5-11D7-A641-000A95A099E0@stanford.edu>

>
Hi,

> One suggestion is to use PRODRG, another is to get partial charges from
> QM, and I've also read that QM charges are too big and should *not* be
> used. PRODRG offers both "full" and "partial"  charges, though I'm not
> sure what these mean exactly.
>

In general, QM charges are great provided they are derived by fitting 
electrostatic potentials (e.g. 'CHELPG' or 'Merz-Kollman' methods in 
Gaussian). Mulliken charges are usually slightly too large for good MD 
results...

Cheers,

Erik



From ramon at fis.unam.mx  Thu Aug 14 04:01:01 2003
From: ramon at fis.unam.mx (=?iso-8859-1?Q?Dr._Ram=F3n_Gardu=F1o-Ju=E1rez?=)
Date: Thu Aug 14 04:01:01 2003
Subject: [gmx-users] =?iso-8859-1?Q?demo=B4s_segmentation_fault?=
Message-ID: <000e01c36207$d528cd60$1421f884@TEOTIHUACAN>

Dear GROMACS users:

I have installed GROMACS v3.1.4 in a Linux cluster with a 2.4.18papikernel where the FFTW -2.1.3.-1 is present.

I have access to the GROMACS program from a remote machine.  The DISPLAY variable points to the cluster machine not to the remote machine address. When I run the demo command I get a "Segmentation fault" message as soon as the demo tries to start the pdb2gmx program. However a window is poped out with the GROMACS legend but the calculation stops.

Any ideas as to what I am doing wrong?...............Much obliged.

Dr. Ram?n Gardu?o-Ju?rez
Centro de Ciencias F?sicas, UNAM
M?xico
Phone (777)3291749, (55)56227749
FAX (777)3291775, (55)56227775
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From s8026264 at sepahan.iut.ac.ir  Thu Aug 14 09:10:01 2003
From: s8026264 at sepahan.iut.ac.ir (s8026264)
Date: Thu Aug 14 09:10:01 2003
Subject: [gmx-users] tip4p or spc for oplsaa?
Message-ID: <20030814033146.M16306@sepahan.iut.ac.ir>

Hi

for oplsaa force field which water model is suitable , spc or tip4p?


good luck

Mojtaba Alaei


From lindahl at stanford.edu  Thu Aug 14 10:06:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Thu Aug 14 10:06:01 2003
Subject: [gmx-users] tip4p or spc for oplsaa?
In-Reply-To: <20030814033146.M16306@sepahan.iut.ac.ir>
Message-ID: <EFD9B1CC-CE2D-11D7-A931-000A95A099E0@stanford.edu>

Hi,

OPLS/AA is parameterized for tip4p (which gives the best result, but is 
slower), although tip3p and SPC give quite good results too - they 
aren't any worse than using spc/tip3p with amber or gromacs forcefields.

Cheers,

Erik


On Wednesday, August 13, 2003, at 08:49 PM, s8026264 wrote:

> Hi
>
> for oplsaa force field which water model is suitable , spc or tip4p?
>
>
> good luck
>
> Mojtaba Alaei
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From feenstra at chem.vu.nl  Thu Aug 14 10:50:02 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug 14 10:50:02 2003
Subject: [gmx-users] palmitoyl
In-Reply-To: <00d101c36123$5c7be940$d83a4a86@fox>
References: <B16CE043598D02408DC7DE5A36B2767C0AA5B7@msgdb01.utad.utoledo.edu> <00d101c36123$5c7be940$d83a4a86@fox>
Message-ID: <3F3A5CCB.7060103@chem.vu.nl>

Xavier Periole wrote:
> palmitoyl
> For the DPP/DPPC problem you just have to modifu the name in the pdb
> file. Substitution within a vi session. Becarefull to modify "DPP_" and not only
> "DPP". The number of caracters is important. 
> 
> For the CYS, you have to define a  new residue CYS with the extra part 
> (palmitoyl). Using existing parameters, the charges by ab initio or existing
> calculations

Or, add palmitoyl to the .rtp database and the desired -S-CO- bond to
the specbonds.dat file (like for Cys-Cys, Cys-Heme and His-Heme).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Thu Aug 14 10:50:03 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug 14 10:50:03 2003
Subject: [gmx-users] position restrain energy in stochastic dynamics
In-Reply-To: <00a901c36119$2f768900$d83a4a86@fox>
References: <Pine.LNX.4.33.0308122245460.14634-100000@rugmd7.chem.rug.nl> <00a901c36119$2f768900$d83a4a86@fox>
Message-ID: <3F3A5D3B.1080704@chem.vu.nl>

Xavier Periole wrote:
> ]> In the prsd.mdp, I used "define = -DPOSRE". So I think I should have
> 
> 
> I think it is -DPOSRES and not -DPOSRE. Could it be the reason ??

Check the .top file, there should be either
#ifdef POSRE
or
#ifdef POSRES
This label must match that on the defines = -D<whatever> line in your .mdp.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From F.Hao at chem.rug.nl  Thu Aug 14 12:21:02 2003
From: F.Hao at chem.rug.nl (F.Hao at chem.rug.nl)
Date: Thu Aug 14 12:21:02 2003
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #932 - 5 msgs
In-Reply-To: <20030814100002.27854.49347.Mailman@hawk.theophys.kth.se>
Message-ID: <Pine.LNX.4.33.0308141203570.5309-100000@rugmd7.chem.rug.nl>

>> In the prsd.mdp, I used "define = -DPOSRE". So I think I should have
>>
>>
>> I think it is -DPOSRES and not -DPOSRE. Could it be the reason ??

>Check the .top file, there should be either
>#ifdef POSRE
>or
>#ifdef POSRES
>This label must match that on the defines = -D<whatever> line in your
>.mdp.

Thanks a lot, Xavier and Anton. Yes, you are right. The thing put in
"defines =" should be the same as in top file. I think I just take the
option given in manual when I write my mdp file for sd. Would it be better
put -DPOSRES in the future manual?

Best

Hao Fan :-)

-------------------------------------------------------------------------
Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands
-------------------------------------------------------------------------



From tccf at epq.ime.eb.br  Thu Aug 14 14:55:01 2003
From: tccf at epq.ime.eb.br (Tanos)
Date: Thu Aug 14 14:55:01 2003
Subject: [gmx-users] Lagevin dynamics
Message-ID: <3F3B8653.8060605@epq.ime.eb.br>

	Hi Folks,
	I am trying to perform a LD in a protein with 608 residues but the 
energy is raising too much and the system is halting. I am not sure of 
using the correct procedure. Could someone send me right sequence of 
comands to prepare a system to a LD dynamics ?????
	Thanks in advance !!!!!!!!
	Tanos C. C. Franca
	IME - Rio de Janeiro - RJ
	Brazil



From zhangw at sinr.ac.cn  Thu Aug 14 15:41:02 2003
From: zhangw at sinr.ac.cn (zhangwei)
Date: Thu Aug 14 15:41:02 2003
Subject: [gmx-users] A question on [ bonds ]
Message-ID: <MSGeNg96TwctPBjxPGs000005a6@msg.sinr.ac.cn>

Hi,all
   I want to simulate a carbon nanotube. If the harmonic bond streching is used to simulate the C-C interation interlayer, how could I write the [ bonds ] directive? Should I find neighbors of every carbon atom, and list them in the [ bonds ] directive? It'll be hard to do it. I didn't find x2top helpful to write the topology of a carbon nanotube.  And is the [ bonds ] directive indispensable? 
   Incidentally, thanks for Anton's answer.

???
 				

????????Wei Zhang
????????zhangw at sinr.ac.cn
??????????2003-08-14




From vdava at davapc1.bioch.dundee.ac.uk  Thu Aug 14 15:59:01 2003
From: vdava at davapc1.bioch.dundee.ac.uk (Daan van Aalten)
Date: Thu Aug 14 15:59:01 2003
Subject: [gmx-users] A question on [ bonds ]
In-Reply-To: <MSGeNg96TwctPBjxPGs000005a6@msg.sinr.ac.cn>
Message-ID: <Pine.LNX.4.33.0308141445400.29096-100000@davapc1.bioch.dundee.ac.uk>

Dear Zhangwei

Would you be able to provide a PDB file of your nanotube - we'd like to
try it with a "large" version of the PRODRG program here.

cheers

Daan



On Thu, 14 Aug 2003, zhangwei wrote:

> Hi,all
>    I want to simulate a carbon nanotube. If the harmonic bond streching is used to simulate the C-C interation interlayer, how could I write the [ bonds ] directive? Should I find neighbors of every carbon atom, and list them in the [ bonds ] directive? It'll be hard to do it. I didn't find x2top helpful to write the topology of a carbon nanotube.  And is the [ bonds ] directive indispensable?
>    Incidentally, thanks for Anton's answer.
>
> ??????
>
>
> ????????????????Wei Zhang
> ????????????????zhangw at sinr.ac.cn
> ????????????????????2003-08-14
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O



From paloureiro at biof.ufrj.br  Thu Aug 14 20:48:01 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Thu Aug 14 20:48:01 2003
Subject: [gmx-users] Group virial
Message-ID: <1060886559.3f3bd81f97c0b@webmail.biof.ufrj.br>

Dear gmx users,

I want to calculate the virial of a group of atoms.
One way would be to rerun the trajectory using a input .tpr and .xtc file that
contains only the group of interest, SOL for instance.
I have used tpbconv to create a SOL.tpr and trjconv to create a SOL.xtc.
The problem is that mdrun -rerun crashes with segmentation fault.
Does anybody know why?

Regards,

Pedro.

--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil 


From asaraujo at if.sc.usp.br  Thu Aug 14 21:59:01 2003
From: asaraujo at if.sc.usp.br (Alexandre Suman de Araujo)
Date: Thu Aug 14 21:59:01 2003
Subject: [gmx-users] Simulation Crashing
Message-ID: <3F3BECF4.3050106@if.sc.usp.br>

Hi GMXers!!!

I'm performing a simulation and after some steps the mdrun cry 
"segmentation fault". In the log file, the lat line has:

Large VCM(group rest):     -0.01344,      0.03897,     -0.02286, 
ekin-cm:     27.09819 (or something like this,with other values, depends 
of my emtol value in the minimization before the MD)

What this mean???? This can be result of some bad values of parameters 
in my .mdp file???
Thanks for everybody

[]'s

-- 
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - S?o Carlos - Brasil




From diegovallejo at mdq.com.ar  Thu Aug 14 23:01:01 2003
From: diegovallejo at mdq.com.ar (DV)
Date: Thu Aug 14 23:01:01 2003
Subject: [gmx-users] Group virial
In-Reply-To: <1060886559.3f3bd81f97c0b@webmail.biof.ufrj.br>
Message-ID: <GFEAICELJBGODAEIMHMOOEOPCFAA.diegovallejo@mdq.com.ar>

Dear gmx devs,

In the pdf Manual says:

7.3.19 Electric fields
E x ; E y ; E z:
	...
E xt; E yt; E zt:
	not implemented yet

Do you have plans in the near future for implementing Time Dependent
Electric Fields?


Thanks

Diego Vallejo  -  vallejo at iflysib.unlp.edu.ar  ++++++++++++++++++++++
Instituto de F?sica de L?quidos y Sistemas Biol?gicos  - UNLP/CONICET
59 N?789  (B1900BTE) La Plata.                                      +
Tel: +54 221 425 4904/ 423 3283  #17    Fax: +54 221 425 7317       +

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From nunolf at ci.uc.pt  Fri Aug 15 17:45:02 2003
From: nunolf at ci.uc.pt (Nuno R. L. Ferreira)
Date: Fri Aug 15 17:45:02 2003
Subject: [gmx-users] Some questions: epsilon_r , DispCorr , g_velacc and PME
Message-ID: <000d01c36342$715abff0$670110ac@gandalf>

Dear * gmx's

My system is composed of protein + solvent.
Some questions are puzzling me, and for a mind seeking rest, nothing better
than to solve the problems, or ask for help.

1) If I use a solvent different from water, do I have to change the
*epsilon_r* value and why?
    Read something about it in this mail list, saying to not change the
value .
http://www.gromacs.org/pipermail/gmx-users/2002-September/029287.html
    By the way, I'm using PME.

2) Don't understand the dispersion correction concept.  I just know that to
get the correct density at normal pressure I have to enable this feature.

3) I'm starting to work with autocorrelation functions, namely VACF. Can
anibody give me some hints on how to calculate diffusion coefficients from
this?

4) My protein has zero charge, so I didn't added ions to the system.  If I
add ions maintaining the neutrality of the system, will the results be
different? Of course, trying and compare the results is the best way.
Should I use PME when I don't add ions to the system, or there's no problem
with that?


Thank you,
Nuno

#######
Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Qu?mica Biol?gica
Departamento de Qu?mica
Faculdade de Ci?ncias e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal
www.biolchem.qui.uc.pt
####




From claudio-margulis at uiowa.edu  Fri Aug 15 22:13:01 2003
From: claudio-margulis at uiowa.edu (Claudio J. Margulis)
Date: Fri Aug 15 22:13:01 2003
Subject: [gmx-users] compilation problems under cygwin
Message-ID: <3F3D3E7F.8080808@uiowa.edu>

Can anyone help me with this??
everything goes fine up to this point.
Thanks!

gcc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include  
-I/usr/X11R6/include  -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include/  -O6 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double 
-funroll-all-loops -c `test -f xutils.c || echo './'`xutils.c
cc1: warning: changing search order for system directory 
"/usr/local/include"
cc1: warning:   as it has already been specified as a non-system directory
xutils.c:97: `fmax' redeclared as different kind of symbol
/usr/include/math.h:146: previous declaration of `fmax'
xutils.c:97: warning: `fmax' was declared `extern' and later `static'
make[3]: *** [xutils.o] Error 1
make[3]: Leaving directory `/home/claudiom/gromacs-3.1.4/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/claudiom/gromacs-3.1.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/claudiom/gromacs-3.1.4/src'
make: *** [all-recursive] Error 1

-- 
Claudio J. Margulis
Assistant Professor
Department of Chemistry
University of Iowa
Iowa City, IA 52242




From claudio-margulis at uiowa.edu  Fri Aug 15 22:53:00 2003
From: claudio-margulis at uiowa.edu (Claudio J. Margulis)
Date: Fri Aug 15 22:53:00 2003
Subject: [gmx-users] [Fwd: compilation problems under cygwin]
Message-ID: <3F3D4805.4080407@uiowa.edu>

Can anyone help me with this??

everything goes fine up to this point.
Thanks!

gcc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include  
-I/usr/X11R6/include  -I../../include 
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include/  -O6 
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -malign-double 
-funroll-all-loops -c `test -f xutils.c || echo './'`xutils.c
cc1: warning: changing search order for system directory 
"/usr/local/include"
cc1: warning:   as it has already been specified as a non-system directory
xutils.c:97: `fmax' redeclared as different kind of symbol
/usr/include/math.h:146: previous declaration of `fmax'
xutils.c:97: warning: `fmax' was declared `extern' and later `static'
make[3]: *** [xutils.o] Error 1
make[3]: Leaving directory `/home/claudiom/gromacs-3.1.4/src/kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/claudiom/gromacs-3.1.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/claudiom/gromacs-3.1.4/src'
make: *** [all-recursive] Error 1

-- 
Claudio J. Margulis
Assistant Professor
Department of Chemistry
University of Iowa
Iowa City, IA 52242




-- 
Claudio J. Margulis
Assistant Professor
Department of Chemistry
University of Iowa
Iowa City, IA 52242




From lindahl at stanford.edu  Fri Aug 15 23:02:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Fri Aug 15 23:02:01 2003
Subject: [gmx-users] compilation problems under cygwin
In-Reply-To: <3F3D3E7F.8080808@uiowa.edu>
Message-ID: <EAECD0C3-CF60-11D7-A80C-000A95A099E0@stanford.edu>

Hi Claudio,

Yes, this is a symbol that has been introduced in the Gnu C library 
lately.

Change all occurences of "fmax" in xutils.c to e.g. "gmx_fmax".

(This is already fixed in CVS)

Cheers,

Erik

On Friday, August 15, 2003, at 01:11 PM, Claudio J. Margulis wrote:

> cs.org
>
> Can anyone help me with this??
> everything goes fine up to this point.



From claudio-margulis at uiowa.edu  Sat Aug 16 01:22:00 2003
From: claudio-margulis at uiowa.edu (Claudio J. Margulis)
Date: Sat Aug 16 01:22:00 2003
Subject: [gmx-users] gromacs under cygwin
Message-ID: <3F3D6AD0.6030008@uiowa.edu>

I managed to compile gromacs under cygwin on my laptop and everything 
looks fine (for example ngmx works great)
however when I tried to grompp something I get core dumps. Any idea of 
what went wrong?
Thanks!

This is water from the tutor example

    -maxwarn    int     10  Number of warnings after which input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file grompp003160
Fatal error: Bonded/nonbonded atom type '??w`8?w?????9?wr?w1' not found!




From patra at lorentz.leidenuniv.nl  Sat Aug 16 13:37:01 2003
From: patra at lorentz.leidenuniv.nl (Michael Patra)
Date: Sat Aug 16 13:37:01 2003
Subject: [gmx-users] harmonic angle potential
Message-ID: <200308161135.h7GBZlOW025489@rulilx.lorentz.leidenuniv.nl>

Dear all,

I wounder whether the harmonic angle potential is implemented correctly in
Gromacs. Since the potential is supposed to depend only on the angle, the
computed forces should only try to change that angle. The Gromacs angle 
potential, however, seems to also try to change the bond length. This is seen
when then bond potential is switched off. (For technical reasons, perhaps some
bug, mdrun crashes when evaluating an angle when there are no bonds, so one has
to introduce bonds with a vanishing potential.) One will then see that the
particles connected by the angle are pushed away from each other.

At the end of this message, you will find a short script that will reproduce
this behaviour with Gromacs 3.1.4.

Yours faithfully,

- Michael Patra


#!/bin/sh
cat > grompp.mdp << \EOF
integrator = md
nsteps = 10000
EOF
cat > topol.top << \EOF
[ defaults ]
  1             1               no              1.0     1.0

[ atomtypes ]
    C     1.000      0.000     A  0.0 0.0    ; no vdW interaction
 
[ angletypes ]
 C C C 1 120.0 1.0

[ bondtypes ]
 C C 1 0.5 0.0               ; dummy bond without potential to make mdrun happy
  
[ nonbond_params ]
    C C  1 0.0 0.0

[ moleculetype ]
Carbonstuff 0

[ atoms ]
1       C     1       POL     P1      1       
2       C     1       POL     P2      2       
3       C     1       POL     P3      3       

[ bonds ]
1 2 1
2 3 1

[ angles ]
1 2 3 1

[ system ]
Test of angle routines

[ molecules ]
Carbonstuff 1
EOF
cat > conf.gro << \EOF
Test system
    3
    1POL     P1    1   5.000   4.000   5.000
    1POL     P2    2   5.000   5.000   5.000
    1POL     P3    3   4.000   5.000   5.000
  10.00000  10.00000  10.00000
EOF
grompp
mdrun -v
ngmx


From diegovallejo at mdq.com.ar  Sat Aug 16 15:47:00 2003
From: diegovallejo at mdq.com.ar (DV)
Date: Sat Aug 16 15:47:00 2003
Subject: [gmx-users] gromacs under cygwin
In-Reply-To: <3F3D6AD0.6030008@uiowa.edu>
Message-ID: <GFEAICELJBGODAEIMHMOOEPLCFAA.diegovallejo@mdq.com.ar>

Claudio,

in my own cygwin installation the cpp preprocesor is located in /bin/cpp
rather than /lib/cpp

create a link in /lib/ pointing to /bin/cpp so usual mdp files will run ok.

	cd /bin
	ln /lib/cpp.exe

Saludos
Diego Vallejo  -  vallejo at iflysib.unlp.edu.ar  ++++++++++++++++++++++
Instituto de F?sica de L?quidos y Sistemas Biol?gicos  - UNLP/CONICET
59 N?789  (B1900BTE) La Plata.                                      +
Tel: +54 221 425 4904/ 423 3283  #17    Fax: +54 221 425 7317       +


-----Mensaje original-----
De: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]En
nombre de Claudio J. Margulis
Enviado el: Viernes, 15 de Agosto de 2003 08:21 p.m.
Para: gmx-users
Asunto: [gmx-users] gromacs under cygwin


I managed to compile gromacs under cygwin on my laptop and everything
looks fine (for example ngmx works great)
however when I tried to grompp something I get core dumps. Any idea of
what went wrong?
Thanks!

This is water from the tutor example

    -maxwarn    int     10  Number of warnings after which input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file grompp003160
Fatal error: Bonded/nonbonded atom type '??w`8?w?????9?wr?w1' not found!


_______________________________________________
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From claudio-margulis at uiowa.edu  Sat Aug 16 17:33:00 2003
From: claudio-margulis at uiowa.edu (Claudio J. Margulis)
Date: Sat Aug 16 17:33:00 2003
Subject: [gmx-users] gromacs under cygwin
Message-ID: <3F3E4E7F.2070208@uiowa.edu>

I already had the link, it's something else.
pdb2gmx core dumps.
I just did it all over again, make clean, make, make install,
and it compiles no problem, but if I try pdb2gmx for example
it still core dumps.

The only non standard thing
was changing fmax for gmx_fmax as Erik suggested in
xutils.c

this is when you run grompp on the water example
------------------------------------------------------------------------
      -load string         Releative load capacity of each node on a 
parallel
                            machine. Be sure to use quotes around the 
string,
                            which should contain a number for each node
    -maxwarn    int     10  Number of warnings after which input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file grompp002200
Fatal error: Bonded/nonbonded atom type '??w`8?w?????9?wr?w1' not found!
--------------------------------------------------------------------------------
here is pdb2gmx -f spc216.pdb -o tmp.gro

...
     -dist   real    0.3  Maximum donor-acceptor distance for a H-bond (nm)
    -[no]una   bool     no  Select aromatic rings with united CH atoms on
                            Phenylalanine, Tryptophane and Tyrosine
    -[no]H14   bool     no  Use 1-4 interactions between hydrogen atoms
   -[no]ignh   bool     no  Ignore hydrogen atoms that are in the pdb file
-[no]missing   bool     no  Continue when atoms are missing, dangerous
    -posrefc   real   1000  Force constant for position restraints
      -dummy   enum   none  Convert atoms to dummy atoms: none, hydrogens or
                            aromatics
 -[no]heavyh   bool     no  Make hydrogen atoms heavy
-[no]deuterate bool     no  Change the mass of hydrogens to 2 amu

Reading spc216.pdb...
Segmentation fault (core dumped)
----------------------------------------------------------------------------

Saludos a la gente de la Plata.

Claudio.


-------------------------------------------------------------------------
Claudio,
in my own cygwin installation the cpp preprocesor is located in /bin/cpp
rather than /lib/cpp
create a link in /lib/ pointing to /bin/cpp so usual mdp files will run ok.
cd /bin
ln /lib/cpp.exe
Saludos
Diego Vallejo  -  vallejo at iflysib.unlp.edu.ar  ++++++++++++++++++++++
Instituto de F?sica de L?quidos y Sistemas Biol?gicos  - UNLP/CONICET
59 N?789  (B1900BTE) La Plata.                                      +
Tel: +54 221 425 4904/ 423 3283  #17    Fax: +54 221 425 7317       +

-- 
Claudio J. Margulis
Assistant Professor
Department of Chemistry
University of Iowa
Iowa City, IA 52242




From diegovallejo at mdq.com.ar  Sat Aug 16 17:40:01 2003
From: diegovallejo at mdq.com.ar (DV)
Date: Sat Aug 16 17:40:01 2003
Subject: [gmx-users] gromacs under cygwin
In-Reply-To: <3F3E4E7F.2070208@uiowa.edu>
Message-ID: <GFEAICELJBGODAEIMHMOCEPNCFAA.diegovallejo@mdq.com.ar>

Claudio,

check if file format is unix.

check the file format of your cygwin installation is unix.

Diego Vallejo  -  vallejo at iflysib.unlp.edu.ar  ++++++++++++++++++++++
Instituto de F?sica de L?quidos y Sistemas Biol?gicos  - UNLP/CONICET
59 N?789  (B1900BTE) La Plata.                                      +
Tel: +54 221 425 4904/ 423 3283  #17    Fax: +54 221 425 7317       +


PD: gracias. de donde sos, claudio?




-----Mensaje original-----
De: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]En
nombre de Claudio J. Margulis
Enviado el: S?bado, 16 de Agosto de 2003 12:32 p.m.
Para: gmx-users
Asunto: [gmx-users] gromacs under cygwin


I already had the link, it's something else.
pdb2gmx core dumps.
I just did it all over again, make clean, make, make install,
and it compiles no problem, but if I try pdb2gmx for example
it still core dumps.

The only non standard thing
was changing fmax for gmx_fmax as Erik suggested in
xutils.c

this is when you run grompp on the water example
------------------------------------------------------------------------
      -load string         Releative load capacity of each node on a
parallel
                            machine. Be sure to use quotes around the
string,
                            which should contain a number for each node
    -maxwarn    int     10  Number of warnings after which input processing
                            stops
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file grompp002200
Fatal error: Bonded/nonbonded atom type '??w`8?w?????9?wr?w1' not found!
----------------------------------------------------------------------------
----
here is pdb2gmx -f spc216.pdb -o tmp.gro

...
     -dist   real    0.3  Maximum donor-acceptor distance for a H-bond (nm)
    -[no]una   bool     no  Select aromatic rings with united CH atoms on
                            Phenylalanine, Tryptophane and Tyrosine
    -[no]H14   bool     no  Use 1-4 interactions between hydrogen atoms
   -[no]ignh   bool     no  Ignore hydrogen atoms that are in the pdb file
-[no]missing   bool     no  Continue when atoms are missing, dangerous
    -posrefc   real   1000  Force constant for position restraints
      -dummy   enum   none  Convert atoms to dummy atoms: none, hydrogens or
                            aromatics
 -[no]heavyh   bool     no  Make hydrogen atoms heavy
-[no]deuterate bool     no  Change the mass of hydrogens to 2 amu

Reading spc216.pdb...
Segmentation fault (core dumped)
----------------------------------------------------------------------------

Saludos a la gente de la Plata.

Claudio.


-------------------------------------------------------------------------
Claudio,
in my own cygwin installation the cpp preprocesor is located in /bin/cpp
rather than /lib/cpp
create a link in /lib/ pointing to /bin/cpp so usual mdp files will run ok.
cd /bin
ln /lib/cpp.exe
Saludos
Diego Vallejo  -  vallejo at iflysib.unlp.edu.ar  ++++++++++++++++++++++
Instituto de F?sica de L?quidos y Sistemas Biol?gicos  - UNLP/CONICET
59 N?789  (B1900BTE) La Plata.                                      +
Tel: +54 221 425 4904/ 423 3283  #17    Fax: +54 221 425 7317       +

--
Claudio J. Margulis
Assistant Professor
Department of Chemistry
University of Iowa
Iowa City, IA 52242


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From claudio-margulis at uiowa.edu  Sat Aug 16 19:45:01 2003
From: claudio-margulis at uiowa.edu (Claudio J. Margulis)
Date: Sat Aug 16 19:45:01 2003
Subject: [gmx-users] gromacs under cygwin
Message-ID: <3F3E6D6D.4080200@uiowa.edu>

yes, when I download cygwin I choose unix as file format.
I also thought it could be wrong carriage returns but I don't know...

C.



From spoel at xray.bmc.uu.se  Sun Aug 17 09:13:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Sun Aug 17 09:13:01 2003
Subject: [gmx-users] Group virial
In-Reply-To: <GFEAICELJBGODAEIMHMOOEOPCFAA.diegovallejo@mdq.com.ar>
References: <GFEAICELJBGODAEIMHMOOEOPCFAA.diegovallejo@mdq.com.ar>
Message-ID: <1061104687.1741.4.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-14 at 23:08, DV wrote:
> Dear gmx devs,
> 
> In the pdf Manual says:
> 
> 7.3.19 Electric fields
> E x ; E y ; E z:
> 	...
> E xt; E yt; E zt:
> 	not implemented yet
> 
> Do you have plans in the near future for implementing Time Dependent
> Electric Fields?
yes, it is already on CVS code, although that is not ready for
production yet
> 
> 
> Thanks
> 
> Diego Vallejo  -  vallejo at iflysib.unlp.edu.ar  ++++++++++++++++++++++
> Instituto de F?sica de L?quidos y Sistemas Biol?gicos  - UNLP/CONICET
> 59 N?789  (B1900BTE) La Plata.                                      +
> Tel: +54 221 425 4904/ 423 3283  #17    Fax: +54 221 425 7317       +
> 
> ---
> Outgoing mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
> Version: 6.0.507 / Virus Database: 304 - Release Date: 04/08/2003
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Sun Aug 17 11:36:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Sun Aug 17 11:36:01 2003
Subject: [gmx-users] harmonic angle potential
In-Reply-To: <200308161135.h7GBZlOW025489@rulilx.lorentz.leidenuniv.nl>
References: <200308161135.h7GBZlOW025489@rulilx.lorentz.leidenuniv.nl>
Message-ID: <1061113244.13533.12.camel@h28n2fls34o1123.telia.com>

On Sat, 2003-08-16 at 13:35, Michael Patra wrote:
> Dear all,
> 
> I wounder whether the harmonic angle potential is implemented correctly in
> Gromacs. Since the potential is supposed to depend only on the angle, the
> computed forces should only try to change that angle. The Gromacs angle 
> potential, however, seems to also try to change the bond length. This is seen
> when then bond potential is switched off. (For technical reasons, perhaps some
> bug, mdrun crashes when evaluating an angle when there are no bonds, so one has
> to introduce bonds with a vanishing potential.) One will then see that the
> particles connected by the angle are pushed away from each other.
> 
> At the end of this message, you will find a short script that will reproduce
> this behaviour with Gromacs 3.1.4.
> 
> Yours faithfully,
> 
> - Michael Patra
> 
Dear Michael, 

that was indeed an interesting test case. If you run an energy analysis
you see that you start out with angle energy (= potential) and that
interconverts with the kinetic energy, the total energy is conserved.
This proves that, first the integration algorithm is accurate, and
second that the force is the (correct) negative derivative of the
energy. You can also do a plot of the angle vs. time and you see that
there are large fluctuations due to the fact that you start out with an
angle of 90 while the equilibrium angle is 120. All fine.

It seems that your question is based on a subtle misunderstanding. The
potential is based on the angle indeed, but the forces act in cartesian
space, not in internal coordinates. The forces are computed as the
derivative of the potential with respect to coordinates. From the angle
vs. time plot you can see that the angle equilibrates towards the
specified value, but from ngmx you see that the bonds get much longer.
This is however correct, for the angle potential implemented in gromacs
(and most other programs), because the bond length is not part of the
potential form.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Sun Aug 17 11:40:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Sun Aug 17 11:40:01 2003
Subject: [gmx-users] Some questions: epsilon_r , DispCorr , g_velacc
	and PME
In-Reply-To: <000d01c36342$715abff0$670110ac@gandalf>
References: <000d01c36342$715abff0$670110ac@gandalf>
Message-ID: <1061113477.13538.17.camel@h28n2fls34o1123.telia.com>

On Fri, 2003-08-15 at 17:32, Nuno R. L. Ferreira wrote:
> Dear * gmx's
> 
> My system is composed of protein + solvent.
> Some questions are puzzling me, and for a mind seeking rest, nothing better
> than to solve the problems, or ask for help.
> 
> 1) If I use a solvent different from water, do I have to change the
> *epsilon_r* value and why?
>     Read something about it in this mail list, saying to not change the
> value .
> http://www.gromacs.org/pipermail/gmx-users/2002-September/029287.html
>     By the way, I'm using PME.
epsilon_r should be different from 1 only when using a reaction field.


> 
> 2) Don't understand the dispersion correction concept.  I just know that to
> get the correct density at normal pressure I have to enable this feature.
It corrects for the fact that you have a cut-off of LJ, since the LJ at
long range is always attractive. For SPC water with a cut-off of 0.9 nm
the pressure contribution is -200 bar. Energy is a constant term and not
so important.

> 
> 3) I'm starting to work with autocorrelation functions, namely VACF. Can
> anibody give me some hints on how to calculate diffusion coefficients from
> this?
Doesn't g_velacc do that for you? Otherwise check some textbook like
Allen & Tildesley (that never hurts!)


> 4) My protein has zero charge, so I didn't added ions to the system.  If I
> add ions maintaining the neutrality of the system, will the results be
> different? Of course, trying and compare the results is the best way.
> Should I use PME when I don't add ions to the system, or there's no problem
> with that?
PME is preferred... Ions depends on system size etc., but if your system
is large enough (more than a few thousand waters) I'd recommend adding
ions.


> 
> 
> Thank you,
> Nuno
> 
> #######
> Nuno Ricardo Santos Loureiro da Silva Ferreira
> Grupo de Qu?mica Biol?gica
> Departamento de Qu?mica
> Faculdade de Ci?ncias e Tecnologia
> Universidade de Coimbra
> 3004-535 Coimbra
> Portugal
> www.biolchem.qui.uc.pt
> ####
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Sun Aug 17 11:41:02 2003
From: spoel at xray.bmc.uu.se (David)
Date: Sun Aug 17 11:41:02 2003
Subject: [gmx-users] Simulation Crashing
In-Reply-To: <3F3BECF4.3050106@if.sc.usp.br>
References: <3F3BECF4.3050106@if.sc.usp.br>
Message-ID: <1061113589.13532.20.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-14 at 22:11, Alexandre Suman de Araujo wrote:
> Hi GMXers!!!
> 
> I'm performing a simulation and after some steps the mdrun cry 
> "segmentation fault". In the log file, the lat line has:
> 
> Large VCM(group rest):     -0.01344,      0.03897,     -0.02286, 
> ekin-cm:     27.09819 (or something like this,with other values, depends 
> of my emtol value in the minimization before the MD)
> 
> What this mean???? This can be result of some bad values of parameters 
> in my .mdp file???
> Thanks for everybody

either:
- bad starting structure (most likely)
- incorrect parameters for center of mass motion removal (not so likely)
- temparature coupling parameters.

> 
> []'s
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Sun Aug 17 11:42:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Sun Aug 17 11:42:00 2003
Subject: [gmx-users] Group virial
In-Reply-To: <1060886559.3f3bd81f97c0b@webmail.biof.ufrj.br>
References: <1060886559.3f3bd81f97c0b@webmail.biof.ufrj.br>
Message-ID: <1061113626.13533.22.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-14 at 20:42, Pedro Alexandre Lapido Loureiro wrote:
> Dear gmx users,
> 
> I want to calculate the virial of a group of atoms.
> One way would be to rerun the trajectory using a input .tpr and .xtc file that
> contains only the group of interest, SOL for instance.
> I have used tpbconv to create a SOL.tpr and trjconv to create a SOL.xtc.
> The problem is that mdrun -rerun crashes with segmentation fault.
> Does anybody know why?
tpr might be incorrect. try creating one manually.


> 
> Regards,
> 
> Pedro.
> 
> --
> Pedro Alexandre Lapido Loureiro
> Laborat?rio de F?sica Biol?gica
> Instituto de Biof?sica
> UFRJ
> Brasil 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Sun Aug 17 11:44:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Sun Aug 17 11:44:00 2003
Subject: [gmx-users] A question on [ bonds ]
In-Reply-To: <MSGeNg96TwctPBjxPGs000005a6@msg.sinr.ac.cn>
References: <MSGeNg96TwctPBjxPGs000005a6@msg.sinr.ac.cn>
Message-ID: <1061113730.13538.25.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-14 at 15:40, zhangwei wrote:
> Hi,all
>    I want to simulate a carbon nanotube. If the harmonic bond streching is used to simulate the C-C interation interlayer, how could I write the [ bonds ] directive? Should I find neighbors of every carbon atom, and list them in the [ bonds ] directive? It'll be hard to do it. I didn't find x2top helpful to write the topology of a carbon nanotube.  And is the [ bonds ] directive indispensable? 
>    Incidentally, thanks for Anton's answer.
x2top should work, but you may have to edit the .n2t file slightly.
Furthermore you have to select the right forcefield (only one
supported). I don't know whether the impropers will be OK though.

If prodrg works, thats probably more accurate.

> 
> ???
>  				
> 
> ????????Wei Zhang
> ????????zhangw at sinr.ac.cn
> ??????????2003-08-14
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Sun Aug 17 11:45:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Sun Aug 17 11:45:01 2003
Subject: [gmx-users] infinite systems
In-Reply-To: <Pine.LNX.4.31.0308081940450.29914-100000@lisa.theochem.uni-frankfurt.de>
References: 	 <Pine.LNX.4.31.0308081940450.29914-100000@lisa.theochem.uni-frankfurt.de>
Message-ID: <1061113791.13538.27.camel@h28n2fls34o1123.telia.com>

On Fri, 2003-08-08 at 19:50, Yuguang Mu wrote:
> Dear David,
> I want to simulate  an infinite system, a small peptide in water
> the system is quite small, total 200 atoms.
> if I use normal cut-off, the rcut  has to be smaller than box/2 (around 5
> A), then the simulated system is nonphysical, due to the small cutoff.
> I try to use setenv GMXFULLPBC 1, as:  export GMXFULLPBC=1, then use
> rcut=1nm .
> But the grompp still say it is a error : rcut > box/2.
> What should I do ?

set 
pbc = no
in mdp file
> 
> 
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
> 
> On 31 Jul 2003, David van der Spoel wrote:
> 
> > On Thu, 2003-07-31 at 11:43, Yuguang Mu wrote:
> > > Hi David,
> > > What use is the environment variable:
> > >  setenv GMXFULLPBC 1
> > >
> > > Does it means that the cutoff can be larger than the half of a box ?
> > > Can it be used in Gromacs 3.1.4 ?
> > yes,
> >
> > it means that infinite systems can be treated as well, because gmx
> > computes the periodicity for each interaction separately instead of once
> > per molecule (which is faster).
> > >
> > >
> > > Dr. Yuguang Mu
> > > Institute for Physical and Theoretical Chemistry
> > > J.W. Goethe University Frankfurt am Main
> > > Marie Curie Str. 11
> > > 60439 Frankfurt/Main, Germany
> > > Tel: +49-(0)69-798-29711
> > >
> > > On 31 Jul 2003, David van der Spoel wrote:
> > >
> > > > On Thu, 2003-07-31 at 10:38, Yonggang Gao wrote:
> > > >
> > > > >
> > > > > Hi Anton,
> > > > >
> > > > >
> > > > >
> > > > > I just select one layer graphite about 432 carbon atoms as solute, and
> > > > > the simulation is error when I put it into the water and make it
> > > > > equilibrium. Certainly I have done the minimization. And I?m confused
> > > > > that it is OK if I put the graphite into vacuum without water and
> > > > > simulate it. I don?t know why the water will affect the graphite?s 1-4
> > > > > interaction. I try to select two layer graphite about 864 atoms, and
> > > > > the same problem. Could you help me?
> > > > >
> > > > >
> > > > >
> > > > > Thanks a lot.
> > > >
> > > >
> > > > is this a periodic system? In that case you may want to set an
> > > > environment variable:
> > > > setenv GMXFULLPBC 1
> > > >
> > > > and rerun
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Yonggang
> > > > >
> > > > >
> > > > --
> > > > Groeten, David.
> > > > ________________________________________________________________________
> > > > Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> > > > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > > > phone:	46 18 471 4205		fax: 46 18 511 755
> > > > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From mgrommet at elucidations.net  Mon Aug 18 07:27:00 2003
From: mgrommet at elucidations.net (Mike Grommet)
Date: Mon Aug 18 07:27:00 2003
Subject: [gmx-users] cluster types supported
Message-ID: <007901c36548$ab1d2310$1e00000a@MIKEG>

I have learned from this group that Gromacs cannot utilize an openmosix
cluster...

Can gromacs utilize an openssi cluster, a single system image cluster?

This seems like it might be a FAQ but I had no luck finding information on
the site, or in the mailing list...


Thanks for your help...





From feenstra at chem.vu.nl  Mon Aug 18 10:02:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug 18 10:02:01 2003
Subject: [gmx-users] A question on [ bonds ]
In-Reply-To: <MSGeNg96TwctPBjxPGs000005a6@msg.sinr.ac.cn>
References: <MSGeNg96TwctPBjxPGs000005a6@msg.sinr.ac.cn>
Message-ID: <3F3BA897.1070802@chem.vu.nl>

zhangwei wrote:
> Hi,all
>    I want to simulate a carbon nanotube. If the harmonic bond streching is
> used to simulate the C-C interation interlayer, how could I write the [ bonds ]
> directive? 

These nanotubes are usually very regular, so couldn't you count out which
atoms must be bonded to which? Taking e.g. 20 carbons around a 'ring' of
the tube, you would have bonds 1-2, 2-3, ... , 19-20, 20-1 for the
first 'ring', and then something like 1-21, 3-21, 5-23, 7-23 for the bonds
to the next ring. (I'm just guessing at your actual topology, of course.)
It shouldn't be hard to write a script or small program that would spit out
the right bonded atom pairs, given a few parameters like total number of
atoms, nr of atoms in one 'ring', and perpendicular or (semi-)paralell
orientation (w/r to tube axis).


-- 
Groetjes,

Anton
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Mon Aug 18 10:02:03 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug 18 10:02:03 2003
Subject: [gmx-users] Lagevin dynamics
In-Reply-To: <3F3B8653.8060605@epq.ime.eb.br>
References: <3F3B8653.8060605@epq.ime.eb.br>
Message-ID: <3F3BA92B.8010506@chem.vu.nl>

Tanos wrote:
>     Hi Folks,
>     I am trying to perform a LD in a protein with 608 residues but the 
> energy is raising too much and the system is halting. I am not sure of 
> using the correct procedure. Could someone send me right sequence of 
> comands to prepare a system to a LD dynamics ?????

Generally, it would be similar to MD setup procedures, like EM and
position restrained (PR) equilibration. Does your system minimize well in
EM? Can you run a short bit of PR MD, or PR LD?

The behaviour of LD depends on the LD temperature and the friction coefficient.
If you have the friction wrong, your timescale is off and you might have an
effective timestep that is too large.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Mon Aug 18 10:02:05 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug 18 10:02:05 2003
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #932 - 5 msgs
In-Reply-To: <Pine.LNX.4.33.0308141203570.5309-100000@rugmd7.chem.rug.nl>
References: <Pine.LNX.4.33.0308141203570.5309-100000@rugmd7.chem.rug.nl>
Message-ID: <3F3BA9BA.3000309@chem.vu.nl>

F.Hao at chem.rug.nl wrote:
> Thanks a lot, Xavier and Anton. Yes, you are right. The thing put in
> "defines =" should be the same as in top file. I think I just take the
> option given in manual when I write my mdp file for sd. Would it be better
> put -DPOSRES in the future manual?

It should correspond to whatever pdb2gmx writes by default. I can never
remember which that is, POSRES or POSRE. If we're going to change anything
about that, I'd opt for POSRES. It would be nice, if grompp could check
if your defines in the .mdp actually match something in the .top.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Mon Aug 18 10:05:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug 18 10:05:01 2003
Subject: [gmx-users] PRODRG and partial charges
In-Reply-To: <Pine.LNX.4.33.0308131149390.8254-100000@localhost>
References: <Pine.LNX.4.33.0308131149390.8254-100000@localhost>
Message-ID: <3F3BADC1.2080209@chem.vu.nl>

Douglas Ridgway wrote:
> I'm confused about how to assign partial charges. I did some browsing of 
> the archives, so I know this has come up before, and have started to read 
> some papers, but I'm still confused.
[...]
> Do charges need to be parameterized with the rest of a force field?  Will
> they depend on cutoffs, other molecules and such? How do you do this for a
> new molecule? How arbitrary is it? And how do you figure out what results
> to believe?

For a 'quick-and-dirty' guess at charges, I simply look at 'similar' groups
in the existing forcefield. Also, I've been using Gasteiger charges.
These are trivial to get, and come out at the same range as charges of
comparable groups are in the Gromos forcefields.

To answer the rest, yes, charges are an integrated part with all the rest
of the forcefield and can only be parametrized accordingly. They are not
transferable between forcefields. Phylosophies for assigning charges differ
between the (major) forcefields. (This also means LJ parameters are not
transferable, since the combination determines the interaction between
atoms.) In Amber, they are taken from the prescribed 'Resp' procedure.
In Gromos/Gromacs, they are simply another set of adjustable parameters.

You should parametrize on things like liquid density, heat of vaporization,
and partitioning properties. (Which, if done properly, is a lot of work.)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Mon Aug 18 10:05:03 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug 18 10:05:03 2003
Subject: [gmx-users] how to modify Dielectric constant (DC)
In-Reply-To: <5.1.1.5.2.20030813153202.00a73940@mail.clemson.edu>
References: <5.1.1.5.2.20030813151407.00a70ee8@mail.clemson.edu> <5.1.1.5.2.20030813153202.00a73940@mail.clemson.edu>
Message-ID: <3F3BADFB.2030508@chem.vu.nl>

Vivek Raut wrote:
> OK, but how to do that on only some specific part of the box?? ( say a 
> section across y coordinate??)

Not implemented.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Mon Aug 18 10:05:04 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug 18 10:05:04 2003
Subject: [gmx-users] (no subject)
In-Reply-To: <200308131820.h7DIKO229176@bif12.creighton.edu>
References: <200308131820.h7DIKO229176@bif12.creighton.edu>
Message-ID: <3F3BB15F.6070602@chem.vu.nl>

Attila Borics wrote:
> So as I believe I just fitted the backbone of each structure in my trajectory
> to the backbone of reference structure and calculated RMSD for each. Is that right?

That is what it looks like. You can try several things (if you haven't
already). Use g_confrms to compare your original .pdb with the .tpr
file. That should give 0.0 rmsd as well (although, there have been some
quirks with g_confrms). Alternatively, convert the .tpr back to .pdb
(with editconf) and use a program of your choice.

Are you by any chance simulating a multimeric protein? In that case
you may be victim to PBC, with one monomer of the protein on one side
of the box, and another at another side. Check with e.g. rasmol.
In that case, using 'trjconv -nojump', with a reference structure
in which the monomers are still together, should help you out.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From lindahl at stanford.edu  Mon Aug 18 10:09:00 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Mon Aug 18 10:09:00 2003
Subject: [gmx-users] cluster types supported
In-Reply-To: <007901c36548$ab1d2310$1e00000a@MIKEG>
Message-ID: <E9B08DCB-D152-11D7-A4A8-000A95A099E0@stanford.edu>

Hi Mike,

Single-cpu Gromacs runs work great on any system. As for openmosix, 
there is nothing we can do to support it - it is they who don't support 
MPI :-)

However, since parallel molecular dynamics involve a lot of 
communication and is quite sensitive to load balancing you would get 
really bad performance on an openmosix-style cluster. OpenMosix relies 
on moving processes around, and that would be very bad idea when we 
need to communicate with the other processors 10-100 times per second - 
you would always have one CPU falling behind, and then everybody else 
has to wait for that one. In theory I guess it would work well on an 
unloaded cluster (less than one job per cpu), but last time I checked 
mosix didn't support sockets (used for MPI communication).

Big shared memory machines are great with MPI, but quite costly, so 
most people use linux clusters (with or without fast myrinet or scali 
networking)...

Cheers,

Erik





On Sunday, August 17, 2003, at 10:22 PM, Mike Grommet wrote:

> I have learned from this group that Gromacs cannot utilize an openmosix
> cluster...
>
> Can gromacs utilize an openssi cluster, a single system image cluster?
>
> This seems like it might be a FAQ but I had no luck finding 
> information on
> the site, or in the mailing list...
>
>
> Thanks for your help...
>
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From tccf at epq.ime.eb.br  Mon Aug 18 14:59:01 2003
From: tccf at epq.ime.eb.br (Tanos)
Date: Mon Aug 18 14:59:01 2003
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #937 - 8 msgs
In-Reply-To: <20030818100001.28593.37074.Mailman@hawk.theophys.kth.se>
References: <20030818100001.28593.37074.Mailman@hawk.theophys.kth.se>
Message-ID: <3F40CD59.8070708@epq.ime.eb.br>

    Dear Anton,
    I am afraid I didn't understood properly the LD. My system runs well 
the EM but how could I perform a PR LD if LD is done only in vacuum ????
    I am trying to change tmeperature and friction coefficient values 
but it didn't workout yet. My substrates are jump out the box.
    Thanks a lot.
    Tanos Franca
    IME - Rio de Janeiro - Brazil

> Tanos wrote:
>
>>>     Hi Folks,
>>>     I am trying to perform a LD in a protein with 608 residues but the 
>>> energy is raising too much and the system is halting. I am not sure of 
>>> using the correct procedure. Could someone send me right sequence of 
>>> comands to prepare a system to a LD dynamics ?????
>>    
>>
> Generally, it would be similar to MD setup procedures, like EM and 
> position restrained (PR) equilibration. Does your system minimize well 
> in EM? Can you run a short bit of PR MD, or PR LD? The behaviour of LD 
> depends on the LD temperature and the friction coefficient. If you 
> have the friction wrong, your timescale is off and you might have an 
> effective timestep that is too large.
>




From mgrommet at elucidations.net  Mon Aug 18 16:08:01 2003
From: mgrommet at elucidations.net (Mike Grommet)
Date: Mon Aug 18 16:08:01 2003
Subject: [gmx-users] cluster types supported
References: <E9B08DCB-D152-11D7-A4A8-000A95A099E0@stanford.edu>
Message-ID: <000d01c36591$806f0a90$1e00000a@MIKEG>

Thanks Erik,  I'm pretty much a newbie when it comes to clustering, and
gromacs for that matter..

I appreciate the explanation on the openMosix issue, that really does clear
things up on that front.

And its early, I haven't had my liquid no-doze yet this morning, I'm not
sure if your statement lends weight (or not)
to the openssi cluster question...

Just for reference:   http://www.openssi.org/

Thanks for the response...


M.


----- Original Message -----
From: "Erik Lindahl" <lindahl at stanford.edu>
To: <gmx-users at gromacs.org>
Sent: Monday, August 18, 2003 3:06 AM
Subject: Re: [gmx-users] cluster types supported


> Hi Mike,
>
> Single-cpu Gromacs runs work great on any system. As for openmosix,
> there is nothing we can do to support it - it is they who don't support
> MPI :-)
>
> However, since parallel molecular dynamics involve a lot of
> communication and is quite sensitive to load balancing you would get
> really bad performance on an openmosix-style cluster. OpenMosix relies
> on moving processes around, and that would be very bad idea when we
> need to communicate with the other processors 10-100 times per second -
> you would always have one CPU falling behind, and then everybody else
> has to wait for that one. In theory I guess it would work well on an
> unloaded cluster (less than one job per cpu), but last time I checked
> mosix didn't support sockets (used for MPI communication).
>
> Big shared memory machines are great with MPI, but quite costly, so
> most people use linux clusters (with or without fast myrinet or scali
> networking)...
>
> Cheers,
>
> Erik
>
>
>
>
>
> On Sunday, August 17, 2003, at 10:22 PM, Mike Grommet wrote:
>
> > I have learned from this group that Gromacs cannot utilize an openmosix
> > cluster...
> >
> > Can gromacs utilize an openssi cluster, a single system image cluster?
> >
> > This seems like it might be a FAQ but I had no luck finding
> > information on
> > the site, or in the mailing list...
> >
> >
> > Thanks for your help...
> >
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From alan at lac.inpe.br  Mon Aug 18 16:39:00 2003
From: alan at lac.inpe.br (Alan Wilter Sousa da Silva)
Date: Mon Aug 18 16:39:00 2003
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #937 - 8 msgs
In-Reply-To: <20030818100001.28593.37074.Mailman@hawk.theophys.kth.se>
References: <20030818100001.28593.37074.Mailman@hawk.theophys.kth.se>
Message-ID: <Pine.LNX.4.53.0308181136330.2170@adastra.nucleo.inpe.br>

Where did you hear that??!!

I've been using openmosix, gromacs and mpi for a couple of years!

On Mon, 18 Aug 2003 gmx-users-request at gromacs.org wrote:
> 
> I have learned from this group that Gromacs cannot utilize an openmosix
> cluster...

--------------------------
Alan Wilter Sousa da Silva
--------------------------
M.Sc - Dep. F?sica - PUC/RJ
D.Sc - IBCCF/UFRJ
Bolsista Pesquisador LAC-INPE
S?o Jos? dos Campos (SP), Brasil
alan at lac.inpe.br
www.lac.inpe.br/~alan



From mgrommet at elucidations.net  Mon Aug 18 18:14:00 2003
From: mgrommet at elucidations.net (Mike Grommet)
Date: Mon Aug 18 18:14:00 2003
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #937 - 8 msgs
References: <20030818100001.28593.37074.Mailman@hawk.theophys.kth.se> <Pine.LNX.4.53.0308181136330.2170@adastra.nucleo.inpe.br>
Message-ID: <001401c365a3$896e7ce0$a186a8c0@AUSMGROMMET>

 From this group...  I set up openmosix (using clusterknoppix at the time)
and couldn't seem to get the processes to migrate around when running them.
I asked about my problem and was led to believe that openMosix wouldn't do
mpi and that I was barking up the wrong tree... Did I get the wrong
impression?

I don't discount the high possibility of user error.  I'm open to
enlightenment :)







----- Original Message -----
From: "Alan Wilter Sousa da Silva" <alan at lac.inpe.br>
To: <gmx-users at gromacs.org>
Sent: Monday, August 18, 2003 9:38 AM
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #937 - 8 msgs


> Where did you hear that??!!
>
> I've been using openmosix, gromacs and mpi for a couple of years!
>
> On Mon, 18 Aug 2003 gmx-users-request at gromacs.org wrote:
> >
> > I have learned from this group that Gromacs cannot utilize an openmosix
> > cluster...
>
> --------------------------
> Alan Wilter Sousa da Silva
> --------------------------
> M.Sc - Dep. F?sica - PUC/RJ
> D.Sc - IBCCF/UFRJ
> Bolsista Pesquisador LAC-INPE
> S?o Jos? dos Campos (SP), Brasil
> alan at lac.inpe.br
> www.lac.inpe.br/~alan
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From lindahl at stanford.edu  Mon Aug 18 18:37:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Mon Aug 18 18:37:01 2003
Subject: [gmx-users] cluster types supported
In-Reply-To: <000d01c36591$806f0a90$1e00000a@MIKEG>
Message-ID: <F921B0AB-D199-11D7-A4A8-000A95A099E0@stanford.edu>

Hi,
>
> I appreciate the explanation on the openMosix issue, that really does 
> clear
> things up on that front.
>
> And its early, I haven't had my liquid no-doze yet this morning, I'm 
> not
> sure if your statement lends weight (or not)
> to the openssi cluster question...
>
> Just for reference:   http://www.openssi.org/
>
> Thanks for the response...
>
I'm a bit skeptical for two reasons:

1. It's a relatively new project. What do you do in two years with your 
cluster if it just dies away? It also requires patching kernels, etc.
2. It tries to make the linux cluster into something different. SSI 
works great on a big shared memory machine, but in this case you are 
going to send lots of data over the network. I'd rather have separate 
boxes and reserve the network traffic for my simulation data.

There are plenty of free linux distributions available to automate the 
cluster installation, e.g. http://www.rocksclusters.org.

Cheers,

Erik



From k24dgyl at morgan.ucs.mun.ca  Mon Aug 18 20:35:01 2003
From: k24dgyl at morgan.ucs.mun.ca (Derrick Guang Yuh Lee)
Date: Mon Aug 18 20:35:01 2003
Subject: [gmx-users] adding water 
In-Reply-To: <3F374685.4050504@chem.rug.nl>
Message-ID: <Pine.OSF.3.95.1030818160240.14703B-100000@plato.ucs.mun.ca>

dear gmx-users

i am working with a DPPC monolayer and i want to add 3000 water molecules
to it. i know that i can used the editconf and genbox commands, but how do
i use them to add that number of water molcules and on a particular side
of the monolayer? thanks for any help available.


 - derrick



 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com
 
"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst." 
                                                              - bruce lee



From ysun at mie.utoronto.ca  Mon Aug 18 21:41:02 2003
From: ysun at mie.utoronto.ca (ysun at mie.utoronto.ca)
Date: Mon Aug 18 21:41:02 2003
Subject: [gmx-users] pull code for speptide : floating exception
In-Reply-To: <Pine.A41.4.42.0308150147250.28964-100000@aixterm3.urz.uni-heidelberg.de>
References: <Pine.A41.4.42.0308150147250.28964-100000@aixterm3.urz.uni-heidelberg.de>
Message-ID: <1061235582.3f412b7e1cb4f@webmail.mie.utoronto.ca>

Dear Frauke 

I tried to modify the file  src/mdlib/pull.c  by covering the two lines:  

 /* while (dr[m] >  0.5*box[m][m])  rvec_dec(dr,box[m]);*/
 /* while (dr[m] < -0.5*box[m][m]) rvec_inc(dr,box[m]);*/

it continued showing error "floating exception".
I am studying this part to find out any other potential bugs.

Thanks!

Sun 



 


Quoting Frauke Meyer <fmeyer at ix.urz.uni-heidelberg.de>:

> Hi Sun,
> >
> > As you advised. I tried to skip -pn -pi, it worked and got output
> results.
> > However, when added -pn -pi in the mdrun, it had error: "floating
> exception"
> > just occurred at the beginning (may be the first step)!
> >
> > YOU mentioned you met this problem, due to step=0 the force equal zero, one
> of
> > the function caused the error, how did you solve your problem at that
> time?
> >
> 
> change the do_afm routine in pull.c:
> the lines that were causing the error in my case were
>   for (i=0;i<pull->pull.n;i++) {
>     /* compute how far the springs are stretched */
>      for (m=DIM-1; m>=0; m--) {
>       while (dr[m] >  0.5*box[m][m])  rvec_dec(dr,box[m]);
>       while (dr[m] < -0.5*box[m][m]) rvec_inc(dr,box[m]);
> 
>       dr[m]=pull->dims[m]*(pull->pull.spring[i][m]-pull->pull.x_unc[i][m]);
>     }
> 
> This is a bug, rvec_dec and rvec_inc change dr, which is anyway
> recalculated in the following line (dr[m]=...)
> So I just skipped the two while lines and everythin worked out finely so
> far. I doubt the correctness of them: why should the spring be less or
> more extended depending ont he box length?
> 
> Good luck,
> Frauke
> --
> Frauke Meyer
> Drug Discovery and Design Center
> Shanghai Institute of Materia Medica
> 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park
> Shanghai 201203
> Tel: +86 21 50806600*1201, Fax: +86 21 50806600*1205
> http://www.dddc.ac.cn, e-mail:frauke.meyer at mpi-bpc.mpg.de
> 
> 
> 




From spoel at xray.bmc.uu.se  Mon Aug 18 21:46:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Mon Aug 18 21:46:01 2003
Subject: [gmx-users] adding water
In-Reply-To: <Pine.OSF.3.95.1030818160240.14703B-100000@plato.ucs.mun.ca>
References: <Pine.OSF.3.95.1030818160240.14703B-100000@plato.ucs.mun.ca>
Message-ID: <1061236257.3898.16.camel@h28n2fls34o1123.telia.com>

On Mon, 2003-08-18 at 20:34, Derrick Guang Yuh Lee wrote:
> dear gmx-users
> 
> i am working with a DPPC monolayer and i want to add 3000 water molecules
> to it. i know that i can used the editconf and genbox commands, but how do
> i use them to add that number of water molcules and on a particular side
> of the monolayer? thanks for any help available.
> 
people tend to do this stuff with genbox and a postprocessing script,
check the mailing list archive 
> 
>  - derrick
> 
> 
> 
>  derrick Lee
>  faculty of Science
>  Memorial University of Newfoundland
>  k24dgyl at mun.ca or derrickglee at hotmail.com
>  
> "a teacher is never a giver of truth - he is a guide, a pointer to the
> truth that each student must find for himself. a good teacher is merely a
> catalyst." 
>                                                               - bruce lee
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From paloureiro at biof.ufrj.br  Mon Aug 18 21:49:00 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Mon Aug 18 21:49:00 2003
Subject: [gmx-users] Group virial
In-Reply-To: <1061113626.13533.22.camel@h28n2fls34o1123.telia.com>
References: <1060886559.3f3bd81f97c0b@webmail.biof.ufrj.br> <1061113626.13533.22.camel@h28n2fls34o1123.telia.com>
Message-ID: <1061235849.3f412c8a02d3f@webmail.biof.ufrj.br>

> > Dear gmx users,
> > 
> > I want to calculate the virial of a group of atoms.
> > One way would be to rerun the trajectory using a input .tpr and .xtc file
> that
> > contains only the group of interest, SOL for instance.
> > I have used tpbconv to create a SOL.tpr and trjconv to create a SOL.xtc.
> > The problem is that mdrun -rerun crashes with segmentation fault.
> > Does anybody know why?

> tpr might be incorrect. try creating one manually.
> 
Dear David,

But how would I do that in a binary file?

Regards,

Pedro.


From asaraujo at if.sc.usp.br  Mon Aug 18 21:53:01 2003
From: asaraujo at if.sc.usp.br (Alexandre Suman de Araujo)
Date: Mon Aug 18 21:53:01 2003
Subject: [gmx-users] Simulation Crashing
In-Reply-To: <1061113589.13532.20.camel@h28n2fls34o1123.telia.com>
References: <3F3BECF4.3050106@if.sc.usp.br> <1061113589.13532.20.camel@h28n2fls34o1123.telia.com>
Message-ID: <3F4131C1.3090706@if.sc.usp.br>

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From k24dgyl at morgan.ucs.mun.ca  Tue Aug 19 02:29:01 2003
From: k24dgyl at morgan.ucs.mun.ca (Derrick Guang Yuh Lee)
Date: Tue Aug 19 02:29:01 2003
Subject: [gmx-users] adding water
In-Reply-To: <1061236257.3898.16.camel@h28n2fls34o1123.telia.com>
Message-ID: <Pine.OSF.3.95.1030818215240.1328A-100000@plato.ucs.mun.ca>

dear gmx-users

i tried the previous advice from david, again thank you for responding,
about adding water molecules to a system by checking the gromacs archive
and searching for information relating to my delema, unfortunately i
cannot find this reference, so again, i will ask for some help in either
finding this reference or someone whom can give me the appropriate
commands.

i am working with a system of 40 DPPC lipids, it is set up in a monolayer
and i want to add 3000 water molecules below the layer. if i am correct,
the addition of the 3000 water molecules can be done via genbox command,
unfortunately, i do not know the appropriate command to add the water
molecules or have then underneath my DPPC monolayer. again, if anyone can
help, it would be appreciated.


sincerely

 - derrick



 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com
 
"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst." 
                                                              - bruce lee

On 18 Aug 2003, David wrote:

> On Mon, 2003-08-18 at 20:34, Derrick Guang Yuh Lee wrote:
> > dear gmx-users
> > 
> > i am working with a DPPC monolayer and i want to add 3000 water molecules
> > to it. i know that i can used the editconf and genbox commands, but how do
> > i use them to add that number of water molcules and on a particular side
> > of the monolayer? thanks for any help available.
> > 
> people tend to do this stuff with genbox and a postprocessing script,
> check the mailing list archive 
> > 
> >  - derrick
> > 
> > 
> > 
> >  derrick Lee
> >  faculty of Science
> >  Memorial University of Newfoundland
> >  k24dgyl at mun.ca or derrickglee at hotmail.com
> >  
> > "a teacher is never a giver of truth - he is a guide, a pointer to the
> > truth that each student must find for himself. a good teacher is merely a
> > catalyst." 
> >                                                               - bruce lee
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> -- 
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 



From dallas.warren at vcp.monash.edu.au  Tue Aug 19 03:14:01 2003
From: dallas.warren at vcp.monash.edu.au (Dallas Warren)
Date: Tue Aug 19 03:14:01 2003
Subject: [gmx-users] adding water
In-Reply-To: <Pine.OSF.3.95.1030818215240.1328A-100000@plato.ucs.mun.ca>
References: <1061236257.3898.16.camel@h28n2fls34o1123.telia.com>
Message-ID: <5.1.0.14.2.20030819105729.022addc8@mail1.monash.edu.au>


>unfortunately, i do not know the appropriate command to add the water
>molecules or have then underneath my DPPC monolayer. again, if anyone can
>help, it would be appreciated.

There isn't one within the GROMACS tools.  You need to make your own script 
to either add the waters or remove those added by genbox in the incorrect 
place.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
--------------------------------------------------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
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From k24dgyl at morgan.ucs.mun.ca  Tue Aug 19 03:35:01 2003
From: k24dgyl at morgan.ucs.mun.ca (Derrick Guang Yuh Lee)
Date: Tue Aug 19 03:35:01 2003
Subject: [gmx-users] adding water
In-Reply-To: <5.1.0.14.2.20030819105729.022addc8@mail1.monash.edu.au>
Message-ID: <Pine.OSF.3.95.1030818230222.14521A-100000@plato.ucs.mun.ca>

dear dallas

thank you for the information, a quick question about it. tbere would be
no problem with removing the water molecules added by genbox, but how do i
add the water molecules? and is there any way to control how many are
added? thanks again.


 - derrick



 derrick Lee
 faculty of Science
 Memorial University of Newfoundland
 k24dgyl at mun.ca or derrickglee at hotmail.com
 
"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
catalyst." 
                                                              - bruce lee

On Tue, 19 Aug 2003, Dallas Warren wrote:

> 
> >unfortunately, i do not know the appropriate command to add the water
> >molecules or have then underneath my DPPC monolayer. again, if anyone can
> >help, it would be appreciated.
> 
> There isn't one within the GROMACS tools.  You need to make your own script 
> to either add the waters or remove those added by genbox in the incorrect 
> place.
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
> 



From dallas.warren at vcp.monash.edu.au  Tue Aug 19 03:50:02 2003
From: dallas.warren at vcp.monash.edu.au (Dallas Warren)
Date: Tue Aug 19 03:50:02 2003
Subject: [gmx-users] adding water
In-Reply-To: <Pine.OSF.3.95.1030818230222.14521A-100000@plato.ucs.mun.ca>
References: <5.1.0.14.2.20030819105729.022addc8@mail1.monash.edu.au>
Message-ID: <5.1.0.14.2.20030819113859.00b7c4b0@mail1.monash.edu.au>

Derrick,

>thank you for the information, a quick question about it. tbere would be
>no problem with removing the water molecules added by genbox, but how do i
>add the water molecules? and is there any way to control how many are
>added? thanks again.

With genbox you can specify now many molecules are added using the "-nmol" 
switch, and don't use "-cs", but "-ci" for the water molecule  But they 
will be spread throughout the entire box, except where other molecules are 
located.  So you probably have to add more than you actually want in there, 
depending on the ratio in the box volume above and below the monolayer i.e. 
if it was dead center then adding double the number of water molecules 
should approximately put the right number below it.

Or, you would need to write a script that adds them yourself.  I haven't 
done this myself, but a colleague here has written one that inserts 
molecules randomly into a given box (the random molecule engine with genbox 
has some problems).  Wouldn't be too much of an issue to add constraints on 
the region within the box to place them  You would just have to specify the 
coordinate file to insert them into, the coordinate file for the water 
molecule, how many to insert, and the allowable regions of the box i.e. 
where the "bottom" of the monolayer is located.  How you do this code wise, 
well, best idea I suppose is look at the coding for genbox.

Hope this helps.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
--------------------------------------------------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
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From senthilk at engin.umich.edu  Tue Aug 19 04:26:01 2003
From: senthilk at engin.umich.edu (Senthil Kandasamy)
Date: Tue Aug 19 04:26:01 2003
Subject: [gmx-users] Re : adding water
Message-ID: <1061259948.12200.15.camel@sandwedge>

dear gmx-users

i am working with a DPPC monolayer and i want to add 3000 water
molecules
to it. i know that i can used the editconf and genbox commands, but how
do
i use them to add that number of water molcules and on a particular side
of the monolayer? thanks for any help available.


 - derrick


Hi derrick, 

If I understand you correctly, you want to add a layer of water beneath
a dppc monolayer with 40 lipids. I assume that you know the dimensions
of the DPPC box in the x and y and Z directions. What are the x and y
values?  For 40 lipids, it is likely to be approximately sqrt(40*~62.5)=
5.0nm x 5.0 nm or approximately those dimensions. Now, create a water
box with the same x and y values. genbox -cs -box 5 5 z-value -o
waterin.pdb. You will have to choose the z-value appropriately to get
the necessary number of water molecules. For 3000 molecules, with
x=y=5nm, z is likely to be ~3.8 nm. This generates a water box with the
same x and y dimensions as the DPPC box. Now, all you have to do is use
editconf to recenter your dppc box and water box appropriately and merge
the pdb files. 

e.g. assume DPPC box size is 5x5x3 nm and the created water box size is
5x5x4nm. You can use 

editconf -f dppcin.pdb -o dppcout.pdb -center 0 0 0  and
editconf -f waterin.pdb -o waterout.pdb -center 0 0 -3.5 

Then, if you merge dppcout.pdb and waterout.pdb, you will get what you
are looking for. Of course, you will have to energy minimize this system
and then run a equilibration stage to get a reasonable starting
structure.

Hope this answer was helpful.

Senthil



From sridhar at www.cdfd.org.in  Tue Aug 19 07:57:00 2003
From: sridhar at www.cdfd.org.in (Mr.Sridhar)
Date: Tue Aug 19 07:57:00 2003
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #938 - 12 msgs
In-Reply-To: <20030819011401.6294.53284.Mailman@hawk.theophys.kth.se>
Message-ID: <Pine.SGI.4.44.0308191037190.59759-100000@www.cdfd.org.in>

Dear GMX users,

Iam doing MD on a protein containing heme cofactor.  But some
of the bond types, bond angles and dihedral angles in the heme are not
getting recognised. The folowing warnings were displayed.

#########################################
No default G96Bond types, using zeroes.
No default G96Angle types, using zeroes.
No default Proper Dih. types, using zeroes.
###########################################

The bond type that is not recognised was between SG of CYS in protein  and
FE of HEME.
The angle types that were not recognised were between SG-FE-NR; SG of CYS
FE and NR of HEME.
The dihedral type that were not recognised was between CH1-CH2-SG-FE ;
CH1, CH2 of CYS and FE of HEME

The dynamics ran succesfully, but I doubt this usage of zeroes for these
types would affect correct running of Simulation.

I'll be very grateful to you if you suggest me how to overcome this
problem.


Thank you.

sridhar



From feenstra at chem.vu.nl  Tue Aug 19 09:08:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 19 09:08:01 2003
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #937 - 8 msgs
In-Reply-To: <3F40CD59.8070708@epq.ime.eb.br>
References: <20030818100001.28593.37074.Mailman@hawk.theophys.kth.se> <3F40CD59.8070708@epq.ime.eb.br>
Message-ID: <3F40F4C7.4010900@chem.vu.nl>

Tanos wrote:
>    Dear Anton,
>    I am afraid I didn't understood properly the LD. My system runs well 
> the EM but how could I perform a PR LD if LD is done only in vacuum ????

Put on position restraints, then run LD.

>    I am trying to change tmeperature and friction coefficient values but 
> it didn't workout yet. My substrates are jump out the box.

Check messages by Berk Hess on this list, he suggested some good starting
values for the friction coefficient. Temperature normally should be around
300K, and timesteps at 2 fs (0.002ps).

Is your substrate jumping out of the box not simply a PBC issue?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Tue Aug 19 09:08:03 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Tue Aug 19 09:08:03 2003
Subject: [gmx-users] Some questions: epsilon_r , DispCorr , g_velacc	and
 PME
In-Reply-To: <1061113477.13538.17.camel@h28n2fls34o1123.telia.com>
References: <000d01c36342$715abff0$670110ac@gandalf> <1061113477.13538.17.camel@h28n2fls34o1123.telia.com>
Message-ID: <3F40F7E4.5030502@chem.vu.nl>

David wrote:
> On Fri, 2003-08-15 at 17:32, Nuno R. L. Ferreira wrote:
> 
>>Dear * gmx's
[...]
>>3) I'm starting to work with autocorrelation functions, namely VACF. Can
>>anibody give me some hints on how to calculate diffusion coefficients from
>>this?
> 
> Doesn't g_velacc do that for you? Otherwise check some textbook like
> Allen & Tildesley (that never hurts!)

To get accurate diffusion from the vacc, you will need velocities on every
md step (i.e. every 2 fs!). Usually, that means writing a lot of data,
since you will still need, for most systems, several 100ps of simulation
to get converged systems. (I've had some students work on this once.)

If you work out the maths, you see that the integral of your VACF is exactly
the same as the slope of the positional MSD (or something similar), from both
you get your diffusion coefficient, which means that mdrun actually can do
the (accurate!) integration for you!


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From mhuhtala at abo.fi  Tue Aug 19 09:40:01 2003
From: mhuhtala at abo.fi (Mikko Huhtala)
Date: Tue Aug 19 09:40:01 2003
Subject: [gmx-users] cluster types supported
In-Reply-To: <20030819011401.6294.53284.Mailman@hawk.theophys.kth.se>
References: <20030819011401.6294.53284.Mailman@hawk.theophys.kth.se>
Message-ID: <16193.54277.96910.518080@urquell.abo.fi>

 > From: "Mike Grommet" 
 > 
 > From this group...  I set up openmosix (using clusterknoppix at the time)
 > and couldn't seem to get the processes to migrate around when running them.
 > I asked about my problem and was led to believe that openMosix wouldn't do
 > mpi and that I was barking up the wrong tree... Did I get the wrong
 > impression?
 > 
 > I don't discount the high possibility of user error.  I'm open to
 > enlightenment :)

OpenMosix provides process migration and dynamic load balancing across
clustered computers, but there is no added parallelization or
interprocess communication APIs in openMosix. oM looks like a regular
Linux system to the program; the process migration mechanism tries to
be as transparent as possible. Both MPI and PVM *can* be run on top of
openMosix and they run quite well in practice. MPI applications such
as Gromacs can benefit from oM in a case where another user starts
something on the nodes that are running Gromacs. oM can automatically
migrate these processes out of the way at run-time if there is free
capacity somewhere else in the cluster. MPI processes can also
migrated, but in practice I suspect many people run them locked to
their original nodes and let other things migrate freely.

The advantage of oM is that it looks to the casual user almost like a
single-image system (minus shared memory), so they do not need to
learn to use queuing etc. We have been running both MPI (Gromacs) and
PVM applications on top of oM practically without problems. oM's
stability is quite good; I last rebooted the cluster about a month ago
to upgrade the kernel and the uptime was over four months at that
point.

Mikko



From spoel at xray.bmc.uu.se  Tue Aug 19 10:02:01 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Tue Aug 19 10:02:01 2003
Subject: [gmx-users] Re: gmx-users digest, Vol 1 #938 - 12 msgs
In-Reply-To: <Pine.SGI.4.44.0308191037190.59759-100000@www.cdfd.org.in>
References: <Pine.SGI.4.44.0308191037190.59759-100000@www.cdfd.org.in>
Message-ID: <1061279910.1135.1.camel@localhost.localdomain>

On Tue, 2003-08-19 at 20:29, Mr.Sridhar wrote:
> Dear GMX users,
> 
> Iam doing MD on a protein containing heme cofactor.  But some
> of the bond types, bond angles and dihedral angles in the heme are not
> getting recognised. The folowing warnings were displayed.
> 
> #########################################
> No default G96Bond types, using zeroes.
> No default G96Angle types, using zeroes.
> No default Proper Dih. types, using zeroes.
> ###########################################
> 
> The bond type that is not recognised was between SG of CYS in protein  and
> FE of HEME.
> The angle types that were not recognised were between SG-FE-NR; SG of CYS
> FE and NR of HEME.
> The dihedral type that were not recognised was between CH1-CH2-SG-FE ;
> CH1, CH2 of CYS and FE of HEME
> 
> The dynamics ran succesfully, but I doubt this usage of zeroes for these
> types would affect correct running of Simulation.
> 
> I'll be very grateful to you if you suggest me how to overcome this
> problem.
There are parameters for these interactions in the ffgmx force field
(ffgmxbon.itp). Please add these to your top file.

You definitely don't want bond lengths of zero, so check the distance
between sulphur and iron after simulation.
> 
> 
> Thank you.
> 
> sridhar
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From baaden at smplinux.de  Tue Aug 19 11:35:01 2003
From: baaden at smplinux.de (Marc Baaden)
Date: Tue Aug 19 11:35:01 2003
Subject: [gmx-users] Gromacs job locks up computer (reproducibly)
Message-ID: <200308190934.LAA12942@apex.ibpc.fr>

Hi,

I am currently onto a very strange behaviour of a Gromacs run
on a dual athlon box. The job only used a single processor and
for the second time it locks up the computer without any
error message or distinct sign of what went wrong.

It is a long job, and for the second time it locked the machine
after about 10 days on exactly the same timestep.

As I said, no error message, the machine remains pingable, but
no possibility to login neither via the network nor on the console.
Keyboard is dead.

The gromacs log/data files just stop at that given point.

Has anybody ever experienced something similar ?

  Marc


Some details:
Gromacs version 3.1.4
Dual Athlon MP2600+, 1GB RAM
kernel 2.4.20-smp (Debian)

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217




From andrea.bernini at unisi.it  Tue Aug 19 15:22:00 2003
From: andrea.bernini at unisi.it (Andrea Bernini)
Date: Tue Aug 19 15:22:00 2003
Subject: [gmx-users] Counter ions problem
Message-ID: <3F4224B2.9060400@unisi.it>

Dear GMX users,
	I'm new to Gromacs and I have started playing around with the Spider 
Toxin Peptide tutorial. Everything worked fine, except the chloride ions 
addition. The genion command replaced two water molecules with Cl to 
neutralize the toxin +2 charge, but the ions were placed far away from 
the toxin (on the edge of the box) instead of being placed near some 
positive charge of the peptide (other programs do it this way, like cion 
from AMBER). Is this behavior normal or something went wrong with 
genion? And in that case what is your advice?

Thanks in advance, Andrea.

______________________________________________

Andrea Bernini, D. Phil.
Molecular Biology Dept.
University of Siena
Via Fiorentina 1
53100 Siena, Italy



From paloureiro at biof.ufrj.br  Tue Aug 19 15:42:00 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Tue Aug 19 15:42:00 2003
Subject: [gmx-users] Counter ions problem
In-Reply-To: <3F4224B2.9060400@unisi.it>
References: <3F4224B2.9060400@unisi.it>
Message-ID: <1061300191.3f4227dfc623b@webmail.biof.ufrj.br>

> Dear GMX users,
> 	I'm new to Gromacs and I have started playing around with the Spider 
> Toxin Peptide tutorial. Everything worked fine, except the chloride ions 
> addition. The genion command replaced two water molecules with Cl to 
> neutralize the toxin +2 charge, but the ions were placed far away from 
> the toxin (on the edge of the box) instead of being placed near some 
> positive charge of the peptide (other programs do it this way, like cion 
> from AMBER). Is this behavior normal or something went wrong with 
> genion? And in that case what is your advice?
> 
> Thanks in advance, Andrea.
> 
> 

Maybe you have used the flag "-random  yes" with genion? 

Cheers,
Pedro.

--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil 


From andre at qt.dq.ufscar.br  Tue Aug 19 16:44:01 2003
From: andre at qt.dq.ufscar.br (Andre Farias de Moura)
Date: Tue Aug 19 16:44:01 2003
Subject: [gmx-users] Re : adding water
In-Reply-To: <1061259948.12200.15.camel@sandwedge>
Message-ID: <20030819114411.J49628-100000@qt.dq.ufscar.br>

dear gmx-users,

correct me if I am wrong, but it seems that it is not
necessary to remove any water molecule from the box as
long as you are using periodic boundary conditions. it
does not matter if there seems to be water molecules
above and beneath your monolayer, these molecules
belong together to the same solvent layer. so, derrick,
all you need is to add 3000 water molecules, unless
you are not going to work with periodic boundary conditions,
in which case you will need some scripting.

I hope it helps you.

andre

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
      Andr?? Farias de Moura
  Laborat??rio de Qu??mica Te??rica
Universidade Federal de S??o Carlos
     S??o Carlos - SP - Brasil
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

On 18 Aug 2003, Senthil Kandasamy wrote:

>
> dear gmx-users
>
> i am working with a DPPC monolayer and i want to add 3000 water
> molecules
> to it. i know that i can used the editconf and genbox commands, but how
> do
> i use them to add that number of water molcules and on a particular side
> of the monolayer? thanks for any help available.
>
>
>  - derrick
>
>
> Hi derrick,
>
> If I understand you correctly, you want to add a layer of water beneath
> a dppc monolayer with 40 lipids. I assume that you know the dimensions
> of the DPPC box in the x and y and Z directions. What are the x and y
> values?  For 40 lipids, it is likely to be approximately sqrt(40*~62.5)=
> 5.0nm x 5.0 nm or approximately those dimensions. Now, create a water
> box with the same x and y values. genbox -cs -box 5 5 z-value -o
> waterin.pdb. You will have to choose the z-value appropriately to get
> the necessary number of water molecules. For 3000 molecules, with
> x=y=5nm, z is likely to be ~3.8 nm. This generates a water box with the
> same x and y dimensions as the DPPC box. Now, all you have to do is use
> editconf to recenter your dppc box and water box appropriately and merge
> the pdb files.
>
> e.g. assume DPPC box size is 5x5x3 nm and the created water box size is
> 5x5x4nm. You can use
>
> editconf -f dppcin.pdb -o dppcout.pdb -center 0 0 0  and
> editconf -f waterin.pdb -o waterout.pdb -center 0 0 -3.5
>
> Then, if you merge dppcout.pdb and waterout.pdb, you will get what you
> are looking for. Of course, you will have to energy minimize this system
> and then run a equilibration stage to get a reasonable starting
> structure.
>
> Hope this answer was helpful.
>
> Senthil
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From paloureiro at biof.ufrj.br  Tue Aug 19 18:37:01 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Tue Aug 19 18:37:01 2003
Subject: [gmx-users] Multiple torsional parameters
Message-ID: <1061310725.3f425105c1441@webmail.biof.ufrj.br>

Hi,

I am implementing the lipid force field of Smondyrev & Berkowitz (J Comp Chem 
20, 531 - 1999).
The problem is they use two expressions for one dihedral, such as:
LC2  LC2O    1  0.0   5.8576   3
LC2  LC2O    1 180.0  4.184    1
I have built my .top file in this way.
When I run grompp, there is a warning saying the former parameters will be 
overridden and the latter will be used.
How can I solve this?
(Sorry if a matter like this has been already discussed in the list...)

Cheers,
Pedro.  

--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil 


From periole at inka.mssm.edu  Tue Aug 19 18:38:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Tue Aug 19 18:38:01 2003
Subject: [gmx-users] Gromacs job locks up computer (reproducibly)
References: <200308190934.LAA12942@apex.ibpc.fr>
Message-ID: <015901c36670$22b392b0$d83a4a86@fox>


That's sounds like the famous 2GB problem !! Files too big !!
Cut your simulation in pieces !!! 

XAvier





From periole at inka.mssm.edu  Tue Aug 19 18:43:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Tue Aug 19 18:43:01 2003
Subject: [gmx-users] Counter ions problem
References: <3F4224B2.9060400@unisi.it>
Message-ID: <018f01c36670$e40db620$d83a4a86@fox>

I don't think you want the counter ion interacting with the peptide.
Except if there is a specific binding site, of course. The counter ions 
are there to neutralize the system not to interact with the protein. 
In general you impose the counter ion to be a minimum distance
from the protein and you pray it not to mess up with your protein !!
It can result in big deformations of the protein !!

XAvier





From baaden at smplinux.de  Tue Aug 19 18:46:01 2003
From: baaden at smplinux.de (Marc Baaden)
Date: Tue Aug 19 18:46:01 2003
Subject: [gmx-users] Gromacs job locks up computer (reproducibly) 
In-Reply-To: Your message of "Tue, 19 Aug 2003 12:37:09 EDT."
             <015901c36670$22b392b0$d83a4a86@fox> 
Message-ID: <200308191645.SAA21152@apex.ibpc.fr>

Hi,

it is not the 2GB problem.
The files are all well below 1GB (around 500 MB).

It seems some people have had similar behaviour
on Athlon boxes .. ?

Marc


>>> "Xavier Periole" said:
 >> 
 >> 
 >> That's sounds like the famous 2GB problem !! Files too big !!
 >> Cut your simulation in pieces !!! 
 >> 
 >> XAvier
 >> 
 >> 
 >> 
 >> _______________________________________________
 >> gmx-users mailing list
 >> gmx-users at gromacs.org
 >> http://www.gromacs.org/mailman/listinfo/gmx-users
 >> Please don't post (un)subscribe requests to the list. Use the 
 >> www interface or send it to gmx-users-request at gromacs.org.
 >> 

Marc Baaden

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217




From vraut at CLEMSON.EDU  Tue Aug 19 19:44:00 2003
From: vraut at CLEMSON.EDU (Vivek Raut)
Date: Tue Aug 19 19:44:00 2003
Subject: [gmx-users] how to modify the peptide end groups??
Message-ID: <5.1.1.5.2.20030819133534.00a6a640@mail.clemson.edu>

hi,

i want to change the end groups of GLY (glycine) segment to NH3+ & COO- . I 
tried to modify the ffgmx2.rtp file by adding hydrogens & oxygen as per the 
atom type defined in ffgmx2.atp. But when i try to make a .gro file for the 
peptide, it says that its not abel to match the hydrogens from .hdb &. tdb 
files.

is there a more logical way to modify the end groups?

if not, then how to modify the .hdb & .tdb files??

-------------------------------------------------------------------------------------------------------------------------------------------
Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
--------------------------------------------------------------------------------------------------------------------------------------------



From lindahl at stanford.edu  Tue Aug 19 19:59:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Tue Aug 19 19:59:01 2003
Subject: [gmx-users] Gromacs job locks up computer (reproducibly) 
In-Reply-To: <200308191645.SAA21152@apex.ibpc.fr>
Message-ID: <97A1587E-D26E-11D7-BC0E-000A95A099E0@stanford.edu>

If it's an amd,

1. Check if you can repeat it when compiling the standard gromacs 
source (necessary for me to debug it, sorry :-)
2. cat /proc/cpuinfo and send it to me.
3. Try to find a file that crashes as soon as possible (30 minutes is 
ok, 24 hours bad)
4. Describe it well as you can.


Some background:

This is almost certainly a hardware problem in the AMD SSE 
implementation. That is probably possible to work around, but the 
results seem to change between different generations of the Athlon 
CPUs, so it has been almost impossible for me to debug.

A fix (which will probably be an environment variable soon) is to edit 
src/gmxlib/detectcpu.c and disable the SSE checking on your Athlon, 
That way it will always use 3DNow, which is about 10% slower but rock 
stable.

I'm sorry for the problems, but the Athlons and Pentiums are executing 
*identical* code, and we've never seen a problem on the latter!

Cheers,

Erik





On Tuesday, August 19, 2003, at 09:45 AM, Marc Baaden wrote:

>
> Hi,
>
> it is not the 2GB problem.
> The files are all well below 1GB (around 500 MB).
>
> It seems some people have had similar behaviour
> on Athlon boxes .. ?
>
> Marc
>
>
>>>> "Xavier Periole" said:
>>>
>>>
>>> That's sounds like the famous 2GB problem !! Files too big !!
>>> Cut your simulation in pieces !!!
>>>
>>> XAvier
>>>
>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list
>>> gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>>
>
> Marc Baaden
>
> -- 
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
>  FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From mceruso at physbio.mssm.edu  Tue Aug 19 20:07:00 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Tue Aug 19 20:07:00 2003
Subject: [gmx-users] how to modify the peptide end groups??
In-Reply-To: <5.1.1.5.2.20030819133534.00a6a640@mail.clemson.edu>
Message-ID: <IGEALMIPJBHPAJBIPPJEAECPCAAA.mceruso@physbio.mssm.edu>

pdb2gmx will add the end groups for you without any need to modify .rtp
etc...


Marc
-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Vivek Raut
Sent: Tuesday, August 19, 2003 1:41 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] how to modify the peptide end groups??


hi,

i want to change the end groups of GLY (glycine) segment to NH3+ & COO- . I
tried to modify the ffgmx2.rtp file by adding hydrogens & oxygen as per the
atom type defined in ffgmx2.atp. But when i try to make a .gro file for the
peptide, it says that its not abel to match the hydrogens from .hdb &. tdb
files.

is there a more logical way to modify the end groups?

if not, then how to modify the .hdb & .tdb files??

----------------------------------------------------------------------------
---------------------------------------------------------------
Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
----------------------------------------------------------------------------
----------------------------------------------------------------

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.




From dbostick at physics.unc.edu  Tue Aug 19 20:16:01 2003
From: dbostick at physics.unc.edu (David L. Bostick)
Date: Tue Aug 19 20:16:01 2003
Subject: [gmx-users] cvs download
Message-ID: <Pine.GSO.4.33.0308191409130.29958-100000@tiberius.physics.unc.edu>

Hello all,

I and many of my colleagues have attempted to download the cvs version of
gromacs very recently and have been unsuccessful.  The 2 commands
recommended by the gromacs website were used:

cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs login
cvs -z3 -d :pserver:anoncvs at cvs.gromacs.org:/home/gmx/cvs co gmx

It seems that upon downloading, the process seems to hang when updating
xpm2ps.c consistently. The last time I tried the user mailing list, someone
replied that the full download worked for them. Thus my questions are:

1) Is there anything wrong with the server?
2) If not, can anyone offer any insight as to what I et al. may be doing
wrong when downloading from cvs?
3) Is there an alternative way that I can download the most recent cvs
version of gromacs (via email, or ftp ... etc)?

Thanks,
David

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-



From vraut at CLEMSON.EDU  Tue Aug 19 21:29:00 2003
From: vraut at CLEMSON.EDU (Vivek Raut)
Date: Tue Aug 19 21:29:00 2003
Subject: [gmx-users] how to make end groups charged??
Message-ID: <5.1.1.5.2.20030819152550.00a69580@mail.clemson.edu>

but by default, it makes the end groups NH2 & COOH. I want to make it 
charged,  what modifications are needed?




 >>>pdb2gmx will add the end groups for you without any need to modify .rtp 
etc... Marc

-----Original Message----- From: gmx-users-admin at gromacs.org 
[mailto:gmx-users-admin at gromacs.org]On Behalf Of Vivek Raut Sent: Tuesday, 
August 19, 2003 1:41 PM To: gmx-users at gromacs.org Subject: [gmx-users] how 
to modify the peptide end groups??

  hi,
  i want to change the end groups of GLY (glycine) segment to NH3+ & COO- . 
I tried to modify the ffgmx2.rtp file by adding hydrogens & oxygen as per 
the atom type defined in ffgmx2.atp. But when i try to make a .gro file for 
the peptide, it says that its not abel to match the hydrogens from .hdb &. 
tdb files. is there a more logical way to modify the end groups? if not, 
then how to modify the .hdb & .tdb files??


-------------------------------------------------------------------------------------------------------------------------------------------
Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
--------------------------------------------------------------------------------------------------------------------------------------------
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From jdanzer at eidogen.com  Tue Aug 19 21:49:01 2003
From: jdanzer at eidogen.com (Joseph F. Danzer)
Date: Tue Aug 19 21:49:01 2003
Subject: [gmx-users] make_ndx seg fault
Message-ID: <1061322460.11515.20.camel@bogus.structuresoflife.com>

I have downloaded gromacs-3.1.4 and compiled it under both RedHat 7.2
and RedHat 7.3. I compiled it with the "--disable-float" option.
On both platforms, I am getting a seg fault while running make_ndx. 

I have a small test case that exposes the problem using crambin,
1crn.pdb.

Here are the steps to generate the problem:

# pdb2gmx_d -f 1crn.pdb -o 1crn.gro -p 1crn.top

I select 0 for the gromacs force field

# editconf_d -f 1crn.gro -o 1crn.gro -d 1.0

#  make_ndx_d -f 1crn.gro -o 1crn.ndx < input_ndx

My input_ndx file looks like:

8 & r 1 2 3 4 5 6 7 8 21 22 23 24 25 26 39 40 41 42 43 44 45 46
name 10 side1c
!10
name 11 side1
8 & r 9 10 11 12 13 14 15 16 31 32 33 34 35 36 37 38
name 12 side2c
!12
name 13 side2
8 & r 17 18 19 20 27 28 29 30
name 14 side3c
!14
name 15 side3
1 & r 1 2 3 4 5 6 7 8 39 40 41 42 43 44 45 46
name 16 main1c
!16
name 17 main1
1 & r 9 10 11 12 13 14 15 16 31 32 33 34 35 36 37 38
name 18 main2c
!18
name 19 main2
1 & r 17 18 19 20 27 28 29 30
name 20 main3c
!20
name 21 main3
name 0 grp0
0&11&0
name 22 grp1
22&13&19
name 23 grp2
23&15&21
name 24 grp3
q


The last few output lines of make_ndx are the following:

Copied index group 0
Copied index group 11
Merged two groups with AND: 409 332 -> 332
Copied index group 0
Merged two groups with AND: 332 409 -> 332
Segmentation fault

I ran this in a debugger, gdb, and got the following stack trace for the
seg fault:

#0  0x403cc1e6 in chunk_free (ar_ptr=0x4047dc80, p=0x8184ac8) at
malloc.c:3242
#1  0x403cc727 in chunk_realloc (ar_ptr=0x4047dc80, oldp=0x8184a60, 
    oldsize=96, nb=104) at malloc.c:3550
#2  0x403cc559 in __libc_realloc (oldmem=0x8184a68, bytes=96) at
malloc.c:3390
#3  0x0805a1a2 in save_realloc (name=0x814536e "block->index", 
    file=0x8145363 "make_ndx.c", line=374, ptr=0x8184a68, size=96)
    at smalloc.c:113
#4  0x0804b11d in copy2block (n=332, index=0x81817f0, block=0x8180cf8)
    at make_ndx.c:374
#5  0x0804d158 in edit_index (atoms=0xbfffe120, x=0x817bb10,
block=0x8180cf8, 
    gn=0xbfffe0b8) at make_ndx.c:848
#6  0x0804d40b in main (argc=1, argv=0xbffff614) at make_ndx.c:913
#7  0x4036b336 in __libc_start_main (main=0x804d1e4 <main>, argc=5, 
    ubp_av=0xbffff614, init=0x8049a54 <_init>, fini=0x81449f0 <_fini>, 
    rtld_fini=0x4000d2fc <_dl_fini>, stack_end=0xbffff60c)
    at ../sysdeps/generic/libc-start.c:129


Any help would be appreciated,

Joe

-- 
Joseph F. Danzer <jdanzer at eidogen.com>



From asaraujo at if.sc.usp.br  Tue Aug 19 22:01:01 2003
From: asaraujo at if.sc.usp.br (Alexandre Suman de Araujo)
Date: Tue Aug 19 22:01:01 2003
Subject: [gmx-users] Problems with Energy Minimization
Message-ID: <3F428533.4010705@if.sc.usp.br>

Hi GMXers!!!

I'm performing an EM of a box with 1 molecule of Calixarene solved in 
acetonitrile using oplsaa force field. The result of minimization is 
that the bonds between C and H in CH3 groups are strained from 1.09 
Angstrons (original value) to 1.73 Angstrons and I'd like to avoid this, 
of course.
 I tried to use hbonds constraits but the algorithm could minimize the box.
 I tried to change some parameters of the minimization but the result 
was the same.
Somebody knows why this behavior of the EM algorithm??? How can I do a 
minimization where the molecules of solvent are moved instead of only H 
atoms???

Thank's and waiting answers

-- 
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - S?o Carlos - Brasil




From mceruso at physbio.mssm.edu  Tue Aug 19 23:09:01 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Tue Aug 19 23:09:01 2003
Subject: [gmx-users] how to make end groups charged??
In-Reply-To: <5.1.1.5.2.20030819152550.00a69580@mail.clemson.edu>
Message-ID: <IGEALMIPJBHPAJBIPPJEAEDACAAA.mceruso@physbio.mssm.edu>


  -----Original Message-----
  From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Vivek Raut
  Sent: Tuesday, August 19, 2003 3:27 PM
  To: gmx-users at gromacs.org
  Subject: [gmx-users] how to make end groups charged??


  but by default, it makes the end groups NH2 & COOH. I want to make it
charged,  what modifications are needed?
  [Marco Ceruso]
  pdb2gmx -f conf.gro -ter  and you should be given a choice of terminii




  >>>pdb2gmx will add the end groups for you without any need to modify .rtp
etc... Marc

  -----Original Message----- From: gmx-users-admin at gromacs.org
[mailto:gmx-users-admin at gromacs.org]On Behalf Of Vivek Raut Sent: Tuesday,
August 19, 2003 1:41 PM To: gmx-users at gromacs.org Subject: [gmx-users] how
to modify the peptide end groups??

   hi,
   i want to change the end groups of GLY (glycine) segment to NH3+ & COO- .
I tried to modify the ffgmx2.rtp file by adding hydrogens & oxygen as per
the atom type defined in ffgmx2.atp. But when i try to make a .gro file for
the peptide, it says that its not abel to match the hydrogens from .hdb &.
tdb files. is there a more logical way to modify the end groups? if not,
then how to modify the .hdb & .tdb files??


  --------------------------------------------------------------------------
-----------------------------------------------------------------
  Vivek Raut
  Graduate Research Assistant
  Department of Bioengineering
  Clemson University
  Clemson, SC- 29631. USA
  Email: vraut at clemson.edu
  Phone: 864-650-1431
  --------------------------------------------------------------------------
------------------------------------------------------------------

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From osmair at qt.dq.ufscar.br  Tue Aug 19 23:21:01 2003
From: osmair at qt.dq.ufscar.br (Osmair Vital de Oliveira)
Date: Tue Aug 19 23:21:01 2003
Subject: [gmx-users] normal modes analysis
Message-ID: <20030819182912.G49461-100000@qt.dq.ufscar.br>

Hi

I tried performed calculation of  normal modes analysis:

g_nmeig -f nm.mtx -s xxx.gro -o -v

but the program complains that:

Reading frame       0 time    0.000   Dimensionality of matrix: 15360
Fatal error: calloc for hess (nelem=235929600, elsize=4, file g_nmeig.c,
line113): Cannot allocate memory

Why?

Thanks

_____________________________________________________________________
---------------------------------------------------------------------
                    Osmair Vital de Oliveira
                           Mestrando

Laboratorio de Quimica Teorica |  Laboratory of Theoretical Chemistry
Departamento de Quimica        |  Departament of Chemistry
                  Universidade Federal de Sao Carlos
                      Sao Carlos - SP - Brazil
                    e-mail: osmair at qt.dq.ufscar.br
_____________________________________________________________________
---------------------------------------------------------------------
                    homepage: www.lqt.dq.ufscar.br



From ygmu at theochem.uni-frankfurt.de  Wed Aug 20 08:36:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Wed Aug 20 08:36:01 2003
Subject: [gmx-users] Multiple torsional parameters
In-Reply-To: <1061310725.3f425105c1441@webmail.biof.ufrj.br>
Message-ID: <Pine.LNX.4.44.0308200829380.19608-100000@marge.theochem.uni-frankfurt.de>

One way is that you can specify one of the torsional in the topological
file, or in the the building unit (residue files), such as

 [ impropers ]
     N    CA    -C     H  improper_X_X_N_H_
then you can define yourself what the improper_X_X_N_H_ can be.A


Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On Tue, 19 Aug 2003, Pedro Alexandre Lapido Loureiro wrote:

> Hi,
>
> I am implementing the lipid force field of Smondyrev & Berkowitz (J Comp Chem
> 20, 531 - 1999).
> The problem is they use two expressions for one dihedral, such as:
> LC2  LC2O    1  0.0   5.8576   3
> LC2  LC2O    1 180.0  4.184    1
> I have built my .top file in this way.
> When I run grompp, there is a warning saying the former parameters will be
> overridden and the latter will be used.
> How can I solve this?
> (Sorry if a matter like this has been already discussed in the list...)
>
> Cheers,
> Pedro.
>
> --
> Pedro Alexandre Lapido Loureiro
> Laborat?rio de F?sica Biol?gica
> Instituto de Biof?sica
> UFRJ
> Brasil
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From phuong at theochem.uni-frankfurt.de  Wed Aug 20 08:54:01 2003
From: phuong at theochem.uni-frankfurt.de (Nguyen Hoang Phuong)
Date: Wed Aug 20 08:54:01 2003
Subject: [gmx-users] normal modes analysis
In-Reply-To: <20030819182912.G49461-100000@qt.dq.ufscar.br>
Message-ID: <Pine.LNX.4.44.0308200849280.19876-100000@marge.theochem.uni-frankfurt.de>

>
> Hi
>
> I tried performed calculation of  normal modes analysis:
>
> g_nmeig -f nm.mtx -s xxx.gro -o -v
>
> but the program complains that:
>
> Reading frame       0 time    0.000   Dimensionality of matrix: 15360
> Fatal error: calloc for hess (nelem=235929600, elsize=4, file g_nmeig.c,
> line113): Cannot allocate memory
>
> Why?

because you don't have enough memory. The Hessian matrix is too large.

>
> Thanks
>
> _____________________________________________________________________
> ---------------------------------------------------------------------
>                     Osmair Vital de Oliveira
>                            Mestrando
>
> Laboratorio de Quimica Teorica |  Laboratory of Theoretical Chemistry
> Departamento de Quimica        |  Departament of Chemistry
>                   Universidade Federal de Sao Carlos
>                       Sao Carlos - SP - Brazil
>                     e-mail: osmair at qt.dq.ufscar.br
> _____________________________________________________________________
> ---------------------------------------------------------------------
>                     homepage: www.lqt.dq.ufscar.br
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From feenstra at chem.vu.nl  Wed Aug 20 08:59:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Wed Aug 20 08:59:01 2003
Subject: [gmx-users] Gromacs job locks up computer (reproducibly)
In-Reply-To: <200308190934.LAA12942@apex.ibpc.fr>
References: <200308190934.LAA12942@apex.ibpc.fr>
Message-ID: <3F42468D.5080102@chem.vu.nl>

Marc Baaden wrote:
> Hi,
> 
> I am currently onto a very strange behaviour of a Gromacs run
> on a dual athlon box. The job only used a single processor and
> for the second time it locks up the computer without any
> error message or distinct sign of what went wrong.
> 
> It is a long job, and for the second time it locked the machine
> after about 10 days on exactly the same timestep.
> 
> As I said, no error message, the machine remains pingable, but
> no possibility to login neither via the network nor on the console.
> Keyboard is dead.
> 
> The gromacs log/data files just stop at that given point.
> 
> Has anybody ever experienced something similar ?

Can't say that I did, but I'll dumb-guess at some possible causes for
this behaviour (this is my usual routine for finding explanations for
strange behaviour ;-). How many steps has your simulation run, i.e. is it
a  very large number like 2^31, 2^32 or 2^63 or so? Have any of the output
files grown to about 2Gb? Does it depend on the output (nst*out) settings?
Is it dependent on the system you simulate? Does it happen on another,
identical, dual athlon? Could you swap CPU's and reproduce the error (i.e.
could it be a faulty CPU)? Does it happen on a non-identical dual athlon?
Is it dependent on memory (type, size, usage), machine load, gromacs
version, compiler options?

P.S. don't start checking all of this if you haven't done it already or
can't do it easily. It's meant as a couple of pointers, one of them might
actually be helpful...?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Wed Aug 20 08:59:03 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Wed Aug 20 08:59:03 2003
Subject: [gmx-users] Group virial
In-Reply-To: <1061235849.3f412c8a02d3f@webmail.biof.ufrj.br>
References: <1060886559.3f3bd81f97c0b@webmail.biof.ufrj.br> <1061113626.13533.22.camel@h28n2fls34o1123.telia.com> <1061235849.3f412c8a02d3f@webmail.biof.ufrj.br>
Message-ID: <3F42484D.1040404@chem.vu.nl>

Pedro Alexandre Lapido Loureiro wrote:
> But how would I do that in a binary file?

Make a modified .top and .gro and use grompp.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Wed Aug 20 08:59:05 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Wed Aug 20 08:59:05 2003
Subject: [gmx-users] Simulation Crashing
In-Reply-To: <3F4131C1.3090706@if.sc.usp.br>
References: <3F3BECF4.3050106@if.sc.usp.br> <1061113589.13532.20.camel@h28n2fls34o1123.telia.com> <3F4131C1.3090706@if.sc.usp.br>
Message-ID: <3F4248CA.1060209@chem.vu.nl>

Alexandre Suman de Araujo wrote:
> Thank you David for your help. I solved the problem making the timestep 
> smaller... I changed it from 1 fs to 0.1 fs and the simulation became stable.
> Thank's for your help.

IMHO, that doesn't sound like a solution... If you need to take 0.1fs
timesteps (2 fs is normal!), there is something *really* wrong in your
system, like David suggested: structure, parameters, temperature, or
possibly your topology.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Wed Aug 20 08:59:07 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Wed Aug 20 08:59:07 2003
Subject: [gmx-users] normal modes analysis
In-Reply-To: <20030819182912.G49461-100000@qt.dq.ufscar.br>
References: <20030819182912.G49461-100000@qt.dq.ufscar.br>
Message-ID: <3F43131F.7000501@chem.vu.nl>

Osmair Vital de Oliveira wrote:
> Hi
> 
> I tried performed calculation of  normal modes analysis:
> 
> g_nmeig -f nm.mtx -s xxx.gro -o -v
> 
> but the program complains that:
> 
> Reading frame       0 time    0.000   Dimensionality of matrix: 15360
> Fatal error: calloc for hess (nelem=235929600, elsize=4, file g_nmeig.c,
> line113): Cannot allocate memory

Unless you have 4*235929600 = about 1Gb of memory, you can't do this.
But, this means you are doing NM on 5120 atoms. Is that what you
really want & need? If this is e.g. a protein, you may want to limit
yourself to backbone, Ca's, or e.g. binding site. Also, even if you
have >1Gb of memory, diagonalizing this matrix (which is what g_nmeig
will do) will be extremely time-consuming.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Wed Aug 20 08:59:09 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Wed Aug 20 08:59:09 2003
Subject: [gmx-users] how to make end groups charged??
In-Reply-To: <5.1.1.5.2.20030819152550.00a69580@mail.clemson.edu>
References: <5.1.1.5.2.20030819152550.00a69580@mail.clemson.edu>
Message-ID: <3F43145D.60001@chem.vu.nl>

Vivek Raut wrote:
> but by default, it makes the end groups NH2 & COOH. I want to make it 
> charged,  what modifications are needed?

Read the pdb2gmx manpage. You can opt for interactive termini selection
(pdb2gmx -ter). You'll get the options you need. No need for editing
the database files.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Wed Aug 20 08:59:11 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Wed Aug 20 08:59:11 2003
Subject: [gmx-users] Multiple torsional parameters
In-Reply-To: <1061310725.3f425105c1441@webmail.biof.ufrj.br>
References: <1061310725.3f425105c1441@webmail.biof.ufrj.br>
Message-ID: <3F431529.50001@chem.vu.nl>

Pedro Alexandre Lapido Loureiro wrote:
> Hi,
> 
> I am implementing the lipid force field of Smondyrev & Berkowitz (J Comp Chem 
> 20, 531 - 1999).
> The problem is they use two expressions for one dihedral, such as:
> LC2  LC2O    1  0.0   5.8576   3
> LC2  LC2O    1 180.0  4.184    1
> I have built my .top file in this way.
> When I run grompp, there is a warning saying the former parameters will be 
> overridden and the latter will be used.
> How can I solve this?
> (Sorry if a matter like this has been already discussed in the list...)

You are probably defining two dihedral *types* for the same pair of atoms.
That won't work. What you will need to do, is add another dihedral to the
.rtp, .itp or .top of your lipid, and specify explicit parameters (or an
explicit type, like in the G43a* ff's) for both of them.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From paloureiro at biof.ufrj.br  Wed Aug 20 14:52:01 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Wed Aug 20 14:52:01 2003
Subject: [gmx-users] Multiple torsional parameters
In-Reply-To: <3F431529.50001@chem.vu.nl>
References: <1061310725.3f425105c1441@webmail.biof.ufrj.br> <3F431529.50001@chem.vu.nl>
Message-ID: <1061383577.3f436d997592e@webmail.biof.ufrj.br>

> Pedro Alexandre Lapido Loureiro wrote:
> > Hi,
> > 
> > I am implementing the lipid force field of Smondyrev & Berkowitz (J Comp
> Chem 
> > 20, 531 - 1999).
> > The problem is they use two expressions for one dihedral, such as:
> > LC2  LC2O    1  0.0   5.8576   3
> > LC2  LC2O    1 180.0  4.184    1
> > I have built my .top file in this way.
> > When I run grompp, there is a warning saying the former parameters will be
> 
> > overridden and the latter will be used.
> > How can I solve this?
> > (Sorry if a matter like this has been already discussed in the list...)
> 
> You are probably defining two dihedral *types* for the same pair of atoms.
> That won't work. What you will need to do, is add another dihedral to the
> .rtp, .itp or .top of your lipid, and specify explicit parameters (or an
> explicit type, like in the G43a* ff's) for both of them.
> 
Thank you, Anton

but that`s exactly what I have done. My .top file is an "explicit type" 
topology file, as long as it contains all the parameters of the force field.
Those two lines I have "pasted" above are from my lipid.top file. And it did 
not work...

Cheers,

Pedro

--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil 


From sridhar at www.cdfd.org.in  Wed Aug 20 15:04:00 2003
From: sridhar at www.cdfd.org.in (Mr.Sridhar)
Date: Wed Aug 20 15:04:00 2003
Subject: [gmx-users] Problems with undefined Bond types, angles and dihedrals
In-Reply-To: <20030819100001.13587.21185.Mailman@hawk.theophys.kth.se>
Message-ID: <Pine.SGI.4.44.0308201834040.16145-100000@www.cdfd.org.in>

ear GMX users,

Iam doing MD on a protein containing heme cofactor.  But some
of the bond types, bond angles and dihedral angles in the heme are not
getting recognised. The folowing warnings were displayed.

#########################################
No default G96Bond types, using zeroes.
No default G96Angle types, using zeroes.
No default Proper Dih. types, using zeroes.
###########################################

The bond type that is not recognised was between SG of CYS in protein  and
FE of HEME.
The angle types that were not recognised were between SG-FE-NR; SG of CYS
FE and NR of HEME.
The dihedral type that were not recognised was between CH1-CH2-SG-FE ;
CH1, CH2 of CYS and FE of HEME

The dynamics ran succesfully, but I doubt this usage of zeroes for these
types would affect correct running of Simulation.

I'll be very grateful to you if you suggest me how to overcome this
problem.


Thank you.

sridhar






From paloureiro at biof.ufrj.br  Wed Aug 20 15:33:00 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Wed Aug 20 15:33:00 2003
Subject: [gmx-users] Multiple torsional parameters
In-Reply-To: <Pine.LNX.4.44.0308200829380.19608-100000@marge.theochem.uni-frankfurt.de>
References: <Pine.LNX.4.44.0308200829380.19608-100000@marge.theochem.uni-frankfurt.de>
Message-ID: <1061386096.3f437770de8e6@webmail.biof.ufrj.br>

> One way is that you can specify one of the torsional in the topological
> file, or in the the building unit (residue files), such as
> 
>  [ impropers ]
>      N    CA    -C     H  improper_X_X_N_H_
> then you can define yourself what the improper_X_X_N_H_ can be.A
> 
> 
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
> 

Thank you for your reply!
But I need two "definitions" for a single dihedral.
This gromacs seems not to accept.

--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil 


From ygmu at theochem.uni-frankfurt.de  Wed Aug 20 16:11:01 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Wed Aug 20 16:11:01 2003
Subject: [gmx-users] Multiple torsional parameters
In-Reply-To: <1061386096.3f437770de8e6@webmail.biof.ufrj.br>
Message-ID: <Pine.LNX.4.31.0308201607310.20204-100000@lisa.theochem.uni-frankfurt.de>

It works, I have tried.

  [ impropers ]
      N    CA    -C     H  improper_X_X_X_X_
  [ impropers ]
      N    CA    -C     H  improper_Y_Y_Y_Y_



Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On Wed, 20 Aug 2003, Pedro Alexandre Lapido Loureiro wrote:

>
> > One way is that you can specify one of the torsional in the topological
> > file, or in the the building unit (residue files), such as
> >
> >  [ impropers ]
> >      N    CA    -C     H  improper_X_X_N_H_
> > then you can define yourself what the improper_X_X_N_H_ can be.A
> >
> >
> > Dr. Yuguang Mu
> > Institute for Physical and Theoretical Chemistry
> > J.W. Goethe University Frankfurt am Main
> > Marie Curie Str. 11
> > 60439 Frankfurt/Main, Germany
> > Tel: +49-(0)69-798-29711
> >
>
> Thank you for your reply!
> But I need two "definitions" for a single dihedral.
> This gromacs seems not to accept.
>
> --
> Pedro Alexandre Lapido Loureiro
> Laborat?rio de F?sica Biol?gica
> Instituto de Biof?sica
> UFRJ
> Brasil
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From arloa at dqb.fcq.unc.edu.ar  Wed Aug 20 16:31:01 2003
From: arloa at dqb.fcq.unc.edu.ar (Marcos Villarreal)
Date: Wed Aug 20 16:31:01 2003
Subject: [gmx-users] Multiple torsional parameters
In-Reply-To: <1061383577.3f436d997592e@webmail.biof.ufrj.br>
References: <1061310725.3f425105c1441@webmail.biof.ufrj.br> <3F431529.50001@chem.vu.nl> <1061383577.3f436d997592e@webmail.biof.ufrj.br>
Message-ID: <03082011314000.14300@fer-net.fcq.unc.edu.ar>

> >You are probably defining two dihedral *types* for the same pair of atoms.
> >That won't work. What you will need to do, is add another dihedral to the
> >.rtp, .itp or .top of your lipid, and specify explicit parameters (or an
> >explicit type, like in the G43a* ff's) for both of them.
> >
> Thank you, Anton
>
> but that`s exactly what I have done. My .top file is an "explicit type"
> topology file, as long as it contains all the parameters of the force
> field. Those two lines I have "pasted" above are from my lipid.top file.
> And it did not work...
>

Dear Pedro,
Try this in your molecule.itp:

[dihedrals]
1  2  3  4    values_A
1  2  3  4    values_B

1 2 3 4  are the numbers of the atoms involved


Saludos,
-- 
Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica - CIQUIBIC.
Universidad Nacional de Cordoba.
Cordoba. Argentina.
http://www.fcq.unc.edu.ar/ciquibic


From gmx3 at hotmail.com  Wed Aug 20 16:32:01 2003
From: gmx3 at hotmail.com (Berk Hess)
Date: Wed Aug 20 16:32:01 2003
Subject: [gmx-users] Re: cvs download
Message-ID: <Law11-F602AhGwEUJlW00068433@hotmail.com>

>It seems that upon downloading, the process seems to hang when updating
>xpm2ps.c consistently. The last time I tried the user mailing list, someone
>replied that the full download worked for them. Thus my questions are:

After (almost) completing cvs checkout, or several other cvs commands, the 
cvs command hangs.
Everything has been done though. xpm2ps.c is the last file, so you have 
checked out the whole
cvs tree.
I have reported this problem to Erik Lindahl three months ago, but it has 
not been fixed yet.

Berk.

_________________________________________________________________
MSN 8 with e-mail virus protection service: 2 months FREE* 
http://join.msn.com/?page=features/virus



From dbostick at physics.unc.edu  Wed Aug 20 16:34:01 2003
From: dbostick at physics.unc.edu (David L. Bostick)
Date: Wed Aug 20 16:34:01 2003
Subject: [gmx-users] cvs download again
Message-ID: <Pine.GSO.4.33.0308201030450.5066-100000@tiberius.physics.unc.edu>

Hello all,

I'm still having problems downloading from cvs ... thought I'd give it a
second try.  Is there any alternative way I can obtain the latest CVS code?

Thanks,
David

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-



From dbostick at physics.unc.edu  Wed Aug 20 16:35:01 2003
From: dbostick at physics.unc.edu (David L. Bostick)
Date: Wed Aug 20 16:35:01 2003
Subject: [gmx-users] Re: cvs download
In-Reply-To: <Law11-F602AhGwEUJlW00068433@hotmail.com>
Message-ID: <Pine.GSO.4.33.0308201033230.5066-100000@tiberius.physics.unc.edu>

Okay thanks Berk!  Coincidentally, I just sent a second message to
gmx-users, so please... all disregard.

David
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

On Wed, 20 Aug 2003, Berk Hess wrote:

> >It seems that upon downloading, the process seems to hang when updating
> >xpm2ps.c consistently. The last time I tried the user mailing list, someone
> >replied that the full download worked for them. Thus my questions are:
>
> After (almost) completing cvs checkout, or several other cvs commands, the
> cvs command hangs.
> Everything has been done though. xpm2ps.c is the last file, so you have
> checked out the whole
> cvs tree.
> I have reported this problem to Erik Lindahl three months ago, but it has
> not been fixed yet.
>
> Berk.
>
> _________________________________________________________________
> MSN 8 with e-mail virus protection service: 2 months FREE*
> http://join.msn.com/?page=features/virus
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From paloureiro at biof.ufrj.br  Wed Aug 20 17:12:00 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Wed Aug 20 17:12:00 2003
Subject: [gmx-users] Multiple torsional parameters
Message-ID: <1061391984.3f438e700f09c@webmail.biof.ufrj.br>




> > >You are probably defining two dihedral *types* for the same pair of
> atoms.
> > >That won't work. What you will need to do, is add another dihedral to
> the
> > >.rtp, .itp or .top of your lipid, and specify explicit parameters (or an
> > >explicit type, like in the G43a* ff's) for both of them.
> > >
> > Thank you, Anton
> >
> > but that`s exactly what I have done. My .top file is an "explicit type"
> > topology file, as long as it contains all the parameters of the force
> > field. Those two lines I have "pasted" above are from my lipid.top file.
> > And it did not work...
> >
>
> Dear Pedro,
> Try this in your molecule.itp:
>
> [dihedrals]
> 1  2  3  4    values_A
> 1  2  3  4    values_B
>
> 1 2 3 4  are the numbers of the atoms involved
>
Thanks, Anton, Marcos and Yuguang Mu!

Yes, it works. 
The problem was my .top file includes the entire forcefield.
So for this to work I had to comment the lines refering to the dihedrals (in 
the ".rtp-like" part of my .top.
Thanks again! 


Cheers,
Pedro.

--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil



From ramon at jl1.quim.ucm.es  Wed Aug 20 18:26:00 2003
From: ramon at jl1.quim.ucm.es (Ramon Garcia Fernandez)
Date: Wed Aug 20 18:26:00 2003
Subject: [gmx-users] Gromacs job locks up computer (reproducibly)
In-Reply-To: <200308190934.LAA12942@apex.ibpc.fr>
References: <200308190934.LAA12942@apex.ibpc.fr>
Message-ID: <20030820162517.GA29493@jl1.quim.ucm.es>

There are known crashes of Athlon boxes with NVidia AGP cards
if you use the drivers from NVidia.

If you do not need hardware accelerated OpenGL you should disable it.

The problem does not happen with normal drivers from XFree86.

Ramon


From vraut at CLEMSON.EDU  Thu Aug 21 04:23:01 2003
From: vraut at CLEMSON.EDU (Vivek Raut)
Date: Thu Aug 21 04:23:01 2003
Subject: [gmx-users] how to fix atoms in bulk?
Message-ID: <5.1.1.5.2.20030820221901.00a70008@mail.clemson.edu>

hi,

i want to fix a group of atoms along a certain height of my water box, is 
there any way how can i fix a group of atoms??

at present, i define a fixgroup & add the atom IDs in that group & then fix 
them in x, y ,z directions.


please help,

vivek

-------------------------------------------------------------------------------------------------------------------------------------------
Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431
--------------------------------------------------------------------------------------------------------------------------------------------



From zhangw at sinr.ac.cn  Thu Aug 21 04:56:01 2003
From: zhangw at sinr.ac.cn (Wei Zhang)
Date: Thu Aug 21 04:56:01 2003
Subject: [gmx-users] Segmentation fault.
Message-ID: <MSGYH7nK48qJXk2C1RC00000f9f@msg.sinr.ac.cn>

Hi,all
    Why when I used the harmonic potential 6, there comes a 'Segmentation fault'? Firstly, I thought it might be caused by a very large force. But when I changed the kb coefficient even to zero, there was still the error. 
	

???
 				

????????Wei Zhang
????????zhangw at sinr.ac.cn
??????????2003-08-21




From periole at inka.mssm.edu  Thu Aug 21 17:39:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Thu Aug 21 17:39:01 2003
Subject: [gmx-users] how to fix atoms in bulk?
References: <5.1.1.5.2.20030820221901.00a70008@mail.clemson.edu>
Message-ID: <002601c367fa$376c1160$d83a4a86@fox>

I guess it is water you want to fix ! I had to do that one and the 
way I turned around the problem was to define a new type of 
water with exactly the same definition as SPC except it was 
called EAU (water in French :)) ). After that all the water molecules
I wanted to be fix had there name changed to EAU and I define
position restrains on them. And you can release the restrains 
afterwards. 

Hope it helps,
XAvier





From bgroot at gwdg.de  Thu Aug 21 17:58:00 2003
From: bgroot at gwdg.de (Bert de Groot)
Date: Thu Aug 21 17:58:00 2003
Subject: [gmx-users] best cluster for gromacs
Message-ID: <3F44EBE4.5A09F418@gwdg.de>

Dear all,

we're about to renew our cluster and I'd like to share our thoughts, and
would very much appreciate if you could share your experience/thoughts too.
There have been some posts on this list about this issue, but there have
been some hardware developments since then, so I figured it would make sense
to post once again. 

So far we've been very happy with our dual athlons (apart from a few stability
issues), but scaling is not that great, especially with PME. We have a few nodes
with myrinet, but even there most jobs run on maximally 2 dual nodes 
(4 processors), because beyond that the scaling simply breaks. We've also
played with gigabit ethernet and the M-VIA protocol, but these only yield
marginal improvements, especially on the faster nodes.

Some points that we considered are:
-the latest generation of SCALI cards seem to have a quite promising 
 price/performance ratio. Does anyone have recent experience with SCALI?
-what about quad Xeon boards?
-any alternative to scali or myrinet for improved low latency networking?
-can we expect developments in gromacs in the near future that will 
 reduce the network load/improve scaling? (I don't want to push the developers
 here, they're doing a splendid job. It's only to optimise the planning).


cheers,

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________


From spoel at xray.bmc.uu.se  Thu Aug 21 18:51:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Thu Aug 21 18:51:01 2003
Subject: [gmx-users] best cluster for gromacs
In-Reply-To: <3F44EBE4.5A09F418@gwdg.de>
References: <3F44EBE4.5A09F418@gwdg.de>
Message-ID: <1061485006.1743.19.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-21 at 17:57, Bert de Groot wrote:
> Dear all,
> 
> we're about to renew our cluster and I'd like to share our thoughts, and
> would very much appreciate if you could share your experience/thoughts too.
> There have been some posts on this list about this issue, but there have
> been some hardware developments since then, so I figured it would make sense
> to post once again. 
> 
Everyone's favorite topic, spending $$$


> So far we've been very happy with our dual athlons (apart from a few stability
> issues), but scaling is not that great, especially with PME. We have a few nodes
> with myrinet, but even there most jobs run on maximally 2 dual nodes 
> (4 processors), because beyond that the scaling simply breaks. We've also
> played with gigabit ethernet and the M-VIA protocol, but these only yield
> marginal improvements, especially on the faster nodes.
> 
> Some points that we considered are:
> -the latest generation of SCALI cards seem to have a quite promising 
>  price/performance ratio. Does anyone have recent experience with SCALI?
Yes, the numbers on the benchmark pages for GROMACS are still valid, but
that is of course for a simulation with a cut-off. We have a 200 node
Xeon/Scali cluster in Link?ping, on which I run reasonably large
simulations (40000 + atoms) with PME routinely on 4 dual processor
nodes. 8 processors is still slightly faster than 6. It seems that the
scali drivers are not optimally stable, but the engineers are working on
it full time. Gromacs scaling is not perfect, but that is mainly a
Gromacs problem. With better algorithms it will improve greatly. 

> -what about quad Xeon boards?
$$$$ and the interconnect (bus) may be not optimal, such that
multiprocessor scaling would be not as good as e.g. IBM.


> -any alternative to scali or myrinet for improved low latency networking?
Didn't Anton report some good results with Gigabit ethernet? Most
machines come with Gigabit nowadays, so it is possible to test first
before forking out $$$ for scali.


> -can we expect developments in gromacs in the near future that will 
>  reduce the network load/improve scaling? (I don't want to push the developers
>  here, they're doing a splendid job. It's only to optimise the planning).
> 
The things Erik is working on will improve performace on any network.
The question is of course whether it is justified to pay the overhead of
fast network card (roughly $300-$400) per machine.

I am personally planning to buy some dual Opteron machines, the main
reason being quantum calculations, but these machines also have a much
superior bus and memory interface compared to Xeons (at least
theoretically). It will be a while before I can do testing though, and
initially I won't buy more than two boxes. According to Erik is the
performance in single precision comparable to similarly clocked P4
machines but you can only get them up until 2 GHz (Xeon to 3 GHz)


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Thu Aug 21 18:52:00 2003
From: spoel at xray.bmc.uu.se (David)
Date: Thu Aug 21 18:52:00 2003
Subject: [gmx-users] how to fix atoms in bulk?
In-Reply-To: <002601c367fa$376c1160$d83a4a86@fox>
References: <5.1.1.5.2.20030820221901.00a70008@mail.clemson.edu>
	 <002601c367fa$376c1160$d83a4a86@fox>
Message-ID: <1061485070.1741.21.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-21 at 17:38, Xavier Periole wrote:
> I guess it is water you want to fix ! I had to do that one and the 
> way I turned around the problem was to define a new type of 
> water with exactly the same definition as SPC except it was 
> called EAU (water in French :)) ). After that all the water molecules
> I wanted to be fix had there name changed to EAU and I define
> position restrains on them. And you can release the restrains 
> afterwards. 

for position restraints you need to do it this way, freezing is group
based, so you only need an index file.
> 
> Hope it helps,
> XAvier
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From sirmoo at cowbert.2y.net  Thu Aug 21 22:42:01 2003
From: sirmoo at cowbert.2y.net (Peter C. Lai)
Date: Thu Aug 21 22:42:01 2003
Subject: [gmx-users] Gromacs job locks up computer (reproducibly)
In-Reply-To: <200308190934.LAA12942@apex.ibpc.fr>
References: <200308190934.LAA12942@apex.ibpc.fr>
Message-ID: <20030821204057.GF1294@cowbert.2y.net>

check that you're not running out of ram and/or swap.

On Tue, Aug 19, 2003 at 11:34:22AM +0200, Marc Baaden wrote:
> 
> Hi,
> 
> I am currently onto a very strange behaviour of a Gromacs run
> on a dual athlon box. The job only used a single processor and
> for the second time it locks up the computer without any
> error message or distinct sign of what went wrong.
> 
> It is a long job, and for the second time it locked the machine
> after about 10 days on exactly the same timestep.
> 
> As I said, no error message, the machine remains pingable, but
> no possibility to login neither via the network nor on the console.
> Keyboard is dead.
> 
> The gromacs log/data files just stop at that given point.
> 
> Has anybody ever experienced something similar ?
> 
>   Marc
> 
> 
> Some details:
> Gromacs version 3.1.4
> Dual Athlon MP2600+, 1GB RAM
> kernel 2.4.20-smp (Debian)
> 
> -- 
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
>  FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.

-- 
Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology
Yale University School of Medicine
SenseLab | Research Assistant
http://cowbert.2y.net/



From malcolm.b.gillies at anu.edu.au  Fri Aug 22 04:36:01 2003
From: malcolm.b.gillies at anu.edu.au (Malcolm Gillies)
Date: Fri Aug 22 04:36:01 2003
Subject: [gmx-users] mdrun crash when -np 8, not when -np 4
Message-ID: <1061519712.24599.16.camel@bakunin>

I have an mdrun job which crashes when I attempt to run it over 8
processors, but which appears to run fine with 4 processors. Any
suggestions?

I'm running Gromacs 3.1.4 on Alpha system. The mdp file and log files
are attached (I'm using PME).

The stack trace on crash:

prun: /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi (pid 13747743) killed by signal 11 (SIGSEGV)
prun: generating backtrace for /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi /local/core/rms/291775/core.mdrun_mpi.sc89.0
Welcome to the Ladebug Debugger Version 67 (built Mar 10 2002 for Compaq Tru64 UNIX)
------------------
object file name: /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
core file name: /local/core/rms/291775/core.mdrun_mpi.sc89.0
Reading symbolic information ...done
Core file produced from executable 'mdrun_mpi'
Thread 8 terminated at PC 0x12010c120 by signal SEGV
Stack trace for thread 8
>0  0x12010c120 in angles(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#1  0x12010ab70 in calc_bonds(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#2  0x1200915d0 in force(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#3  0x120081240 in do_force(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#4  0x12007af54 in do_md(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#5  0x120079b9c in mdrunner(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#6  0x12007cad0 in main(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
#7  0x12006aed8 in __start(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
                                                                                
Stack trace for thread 7
#0  0x3ff801374e8 in __syscall(...) in /usr/shlib/libc.so
#1  0x300010195c0 in elan3_syscall_lwp(ctx=Info: no allocation applies for symbol ctx at the current PC
<no value>) "syscall_dunix.c":201
#2  0x30001007ff8 in elan3_lwp(arg=0x140022800) "elanlib.c":85
                                                                                
prun: dumping elan exception state for /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi /local/core/rms/291775/core.mdrun_mpi.sc89.0
edb: found exception list at 4102bde0
edb: exceptions from '/opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi'
prun:

cheers,

Malcolm
--
Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
John Curtin School of Medical Research, Australian National University
-------------- next part --------------
title               =  MD
cpp                 =  /lib/cpp
constraints         =  hbonds
integrator          =  md
dt                  =  0.001     ; ps !
nsteps              =  1000000   ; total 500 ps.
nstcomm             =  1
nstxout             =  10000
nstvout             =  10000
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.2
rcoulomb            =  1.2
rvdw                =  1.2
coulombtype         =  PME
rcoulomb_switch     =  0.0
dispcorr            =  EnerPres
epsilon_surface     =  78.0
fourierspacing      =  0.1
pmeorder            =  6
optimizefft         =  no
; Nose-Hoover coupling is on in two groups
Tcoupl              =  Nose-Hoover
tau_t               =  0.1      0.1
tc-grps             =  protein  sol
ref_t               =  300      300
; Pressure coupling is on
Pcoupl              =  Parrinello-Rahman
Pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
-------------- next part --------------
Log file opened: nodeid 0, nnodes = 8, host = unknown, process = 13747743
                         :-)  G  R  O  M  A  C  S  (-:

                   GROningen MAchine for Chemical Simulation

                            :-)  VERSION 3.1.4  (-:


       Copyright (c) 1991-2002, University of Groningen, The Netherlands
         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                              :-)  mdrun_mpi  (-:


++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------

CPU=  0, lastcg= 4371, targetcg=21620, myshift=    5
CPU=  1, lastcg= 8677, targetcg=25926, myshift=    5
CPU=  2, lastcg=12980, targetcg=30229, myshift=    5
CPU=  3, lastcg=17283, targetcg=   35, myshift=    5
CPU=  4, lastcg=21586, targetcg= 4338, myshift=    4
CPU=  5, lastcg=25889, targetcg= 8641, myshift=    4
CPU=  6, lastcg=30193, targetcg=12945, myshift=    4
CPU=  7, lastcg=34496, targetcg=17248, myshift=    4
nsb->shift =   5, nsb->bshift=  0
Listing Scalars
nsb->nodeid:         0
nsb->nnodes:      8
nsb->cgtotal: 34497
nsb->natoms:  103277
nsb->shift:       5
nsb->bshift:      0
Nodeid   index  homenr  cgload  workload
     0       0   12910    4372      4372
     1   12910   12910    8678      8678
     2   25820   12909   12981     12981
     3   38729   12909   17284     17284
     4   51638   12909   21587     21587
     5   64547   12909   25890     25890
     6   77456   12912   30194     30194
     7   90368   12909   34497     34497

parameters of the run (nodeid=0):
input record:
   integrator           = md
   nsteps               = 1000000
   ns_type              = Grid
   nstlist              = 10
   ndelta               = 2
   bDomDecomp           = FALSE
   decomp_dir           = 0
   nstcomm              = 1
   nstlog               = 100
   nstxout              = 10000
   nstvout              = 10000
   nstfout              = 0
   nstenergy            = 100
   nstxtcout            = 0
   init_t               = 0
   delta_t              = 0.001
   xtcprec              = 1000
   nkx                  = 96
   nky                  = 112
   nkz                  = 104
   pme_order            = 6
   ewald_rtol           = 1e-05
   ewald_geometry       = 0
   epsilon_surface      = 78
   optimize_fft         = FALSE
   ePBC                 = xyz
   bUncStart            = FALSE
   bShakeSOR            = FALSE
   etc                  = Nose-Hoover
   epc                  = Parrinello-Rahman
   epctype              = Isotropic
   tau_p                = 0.5
   ref_p (3x3):
      ref_p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
      ref_p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      ref_p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   compress (3x3):
      compress[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compress[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compress[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   bSimAnn              = FALSE
   zero_temp_time       = 0
   rlist                = 1.2
   coulombtype          = PME
   rcoulomb_switch      = 0
   rcoulomb             = 1.2
   vdwtype              = Cut-off
   rvdw_switch          = 0
   rvdw                 = 1.2
   epsilon_r            = 1
   DispCorr             = EnerPres
   fudgeQQ              = 0.5
   free_energy          = no
   init_lambda          = 0
   sc_alpha             = 0
   sc_sigma             = 0.3
   delta_lambda         = 0
   disre_weighting      = Conservative
   disre_mixed          = FALSE
   dr_fc                = 1000
   dr_tau               = 0
   nstdisreout          = 100
   orires_fc            = 0
   orires_tau           = 0
   nstorireout          = 100
   em_stepsize          = 0.01
   em_tol               = 100
   niter                = 20
   fc_stepsize          = 0
   nstcgsteep           = 1000
   ConstAlg             = Lincs
   shake_tol            = 0.0001
   lincs_order          = 4
   lincs_warnangle      = 30
   bd_temp              = 300
   bd_fric              = 0
   ld_seed              = 1993
   cos_accel            = 0
   userint1             = 0
   userint2             = 0
   userint3             = 0
   userint4             = 0
   userreal1            = 0
   userreal2            = 0
   userreal3            = 0
   userreal4            = 0
grpopts:
   nrdf:	     42165.4      172852
   ref_t:	         300         300
   tau_t:	         0.1         0.1
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp_excl[  0]: 0
   efield-x:
      n = 0
   efield-xt:
      n = 0
   efield-y:
      n = 0
   efield-yt:
      n = 0
   efield-z:
      n = 0
   efield-zt:
      n = 0
box (3x3):
   box[    0]={ 9.05361e+00,  0.00000e+00,  0.00000e+00}
   box[    1]={ 0.00000e+00,  1.08158e+01,  0.00000e+00}
   box[    2]={ 0.00000e+00,  0.00000e+00,  1.01414e+01}
ekin (3x3):
   ekin[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   ekin[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   ekin[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
pres (3x3):
   pres[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   pres[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   pres[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
vir (3x3):
   vir[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   vir[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   vir[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 4
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Will do PME sum in reciprocal space.

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
   local_nx:                  12  local_x_start:                   0
   local_ny_after_transpose:  14  local_y_start_after_transpose    0
   total_local_size:         142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 639645
There are: 12910 Atom
Removing pbc first time
Done rmpbc

Constraining the starting coordinates (step -2)

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------


Initializing LINear Constraint Solver
  number of constraints is 6446
  average number of constraints coupled to one constraint is 0.9

-------------- next part --------------
Log file opened: nodeid 1, nnodes = 8, host = unknown, process = 13747744
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 4
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 1
There are 2990 optimized water molecules on node 1
Will do PME sum in reciprocal space.

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
   local_nx:                  12  local_x_start:                  12
   local_ny_after_transpose:  14  local_y_start_after_transpose   14
   total_local_size:         142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 639645
There are: 12910 Atom
Removing pbc first time
Done rmpbc

Constraining the starting coordinates (step -2)

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------


Initializing LINear Constraint Solver
  number of constraints is 1938
  average number of constraints coupled to one constraint is 0.9

-------------- next part --------------
Log file opened: nodeid 2, nnodes = 8, host = unknown, process = 13747741
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 2
There are 4303 optimized water molecules on node 2
Will do PME sum in reciprocal space.

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
   local_nx:                  12  local_x_start:                  24
   local_ny_after_transpose:  14  local_y_start_after_transpose   28
   total_local_size:         142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc

Constraining the starting coordinates (step -2)

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------

-------------- next part --------------
Log file opened: nodeid 3, nnodes = 8, host = unknown, process = 13747747
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 3
There are 4303 optimized water molecules on node 3
Will do PME sum in reciprocal space.

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
   local_nx:                  12  local_x_start:                  36
   local_ny_after_transpose:  14  local_y_start_after_transpose   42
   total_local_size:         142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc

Constraining the starting coordinates (step -2)

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------

-------------- next part --------------
Log file opened: nodeid 4, nnodes = 8, host = unknown, process = 14744071
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 4
There are 4303 optimized water molecules on node 4
Will do PME sum in reciprocal space.

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
   local_nx:                  12  local_x_start:                  48
   local_ny_after_transpose:  14  local_y_start_after_transpose   56
   total_local_size:         142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc

Constraining the starting coordinates (step -2)

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------

-------------- next part --------------
Log file opened: nodeid 5, nnodes = 8, host = unknown, process = 14744072
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 5
There are 4303 optimized water molecules on node 5
Will do PME sum in reciprocal space.

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
   local_nx:                  12  local_x_start:                  60
   local_ny_after_transpose:  14  local_y_start_after_transpose   70
   total_local_size:         142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc

Constraining the starting coordinates (step -2)

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------

-------------- next part --------------
Log file opened: nodeid 6, nnodes = 8, host = unknown, process = 14744073
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 6
There are 4304 optimized water molecules on node 6
Will do PME sum in reciprocal space.

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
   local_nx:                  12  local_x_start:                  72
   local_ny_after_transpose:  14  local_y_start_after_transpose   84
   total_local_size:         142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 639645
There are: 12912 Atom
Removing pbc first time
Done rmpbc

Constraining the starting coordinates (step -2)

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------

-------------- next part --------------
Log file opened: nodeid 7, nnodes = 8, host = unknown, process = 14744074
There are 0 atoms for free energy perturbation
Max number of bonds per atom is 2
Table routines are used for coulomb: TRUE
Table routines are used for vdw:     FALSE
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's:   NS: 1.2   Coulomb: 1.2   LJ: 1.2
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 28815 molecules, 34497 charge groups and 103277 atoms
There are 0 optimized solvent molecules on node 7
There are 4303 optimized water molecules on node 7
Will do PME sum in reciprocal space.

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
{A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
PARALLEL FFT DATA:
   local_nx:                  12  local_x_start:                  84
   local_ny_after_transpose:  14  local_y_start_after_transpose   98
   total_local_size:         142464
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest, initial mass: 639645
There are: 12909 Atom
Removing pbc first time
Done rmpbc

Constraining the starting coordinates (step -2)

++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


From spoel at xray.bmc.uu.se  Fri Aug 22 09:08:01 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Fri Aug 22 09:08:01 2003
Subject: [gmx-users] mdrun crash when -np 8, not when -np 4
In-Reply-To: <1061519712.24599.16.camel@bakunin>
References: <1061519712.24599.16.camel@bakunin>
Message-ID: <1061534920.2073.1.camel@localhost.localdomain>

On Fri, 2003-08-22 at 04:35, Malcolm Gillies wrote:
> I have an mdrun job which crashes when I attempt to run it over 8
> processors, but which appears to run fine with 4 processors. Any
> suggestions?
Could it be that you have no water left on processor 0 (which is where I
presume that the problem occurs)?

This is a known bug, which has not been resolved completely yet.

> 
> I'm running Gromacs 3.1.4 on Alpha system. The mdp file and log files
> are attached (I'm using PME).
> 
> The stack trace on crash:
> 
> prun: /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi (pid 13747743) killed by signal 11 (SIGSEGV)
> prun: generating backtrace for /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi /local/core/rms/291775/core.mdrun_mpi.sc89.0
> Welcome to the Ladebug Debugger Version 67 (built Mar 10 2002 for Compaq Tru64 UNIX)
> ------------------
> object file name: /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
> core file name: /local/core/rms/291775/core.mdrun_mpi.sc89.0
> Reading symbolic information ...done
> Core file produced from executable 'mdrun_mpi'
> Thread 8 terminated at PC 0x12010c120 by signal SEGV
> Stack trace for thread 8
> >0  0x12010c120 in angles(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
> #1  0x12010ab70 in calc_bonds(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
> #2  0x1200915d0 in force(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
> #3  0x120081240 in do_force(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
> #4  0x12007af54 in do_md(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
> #5  0x120079b9c in mdrunner(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
> #6  0x12007cad0 in main(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
> #7  0x12006aed8 in __start(...) in /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi
>                                                                                 
> Stack trace for thread 7
> #0  0x3ff801374e8 in __syscall(...) in /usr/shlib/libc.so
> #1  0x300010195c0 in elan3_syscall_lwp(ctx=Info: no allocation applies for symbol ctx at the current PC
> <no value>) "syscall_dunix.c":201
> #2  0x30001007ff8 in elan3_lwp(arg=0x140022800) "elanlib.c":85
>                                                                                 
> prun: dumping elan exception state for /opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi /local/core/rms/291775/core.mdrun_mpi.sc89.0
> edb: found exception list at 4102bde0
> edb: exceptions from '/opt/gromacs-3.1.4nf2/alphaev68-dec-osf5.1/bin/mdrun_mpi'
> prun:
> 
> cheers,
> 
> Malcolm
> --
> Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
> Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
> John Curtin School of Medical Research, Australian National University
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From ygmu at theochem.uni-frankfurt.de  Fri Aug 22 09:16:02 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Fri Aug 22 09:16:02 2003
Subject: [gmx-users] a question
In-Reply-To: <1061534920.2073.1.camel@localhost.localdomain>
Message-ID: <Pine.LNX.4.44.0308220909240.13795-100000@marge.theochem.uni-frankfurt.de>

In the output log file in some case the following line is printed out
(when gromacs is compiled with assembly innerloops)
In other cases without assembly innerloops, this didnot print out.

I am worried about it, because it seems to effects the density of water.

***************************************************************
Going to use C-settle (573 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154,
rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333,
rone = 1, dHH = 0.16333, dOH = 0.1
***************************************************************

Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711




From spoel at xray.bmc.uu.se  Fri Aug 22 09:59:01 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Fri Aug 22 09:59:01 2003
Subject: [gmx-users] a question
In-Reply-To: <Pine.LNX.4.44.0308220909240.13795-100000@marge.theochem.uni-frankfurt.de>
References: 	 <Pine.LNX.4.44.0308220909240.13795-100000@marge.theochem.uni-frankfurt.de>
Message-ID: <1061538098.2073.6.camel@localhost.localdomain>

On Fri, 2003-08-22 at 09:14, Yuguang Mu wrote:
> In the output log file in some case the following line is printed out
> (when gromacs is compiled with assembly innerloops)
> In other cases without assembly innerloops, this didnot print out.
> 
This should not have any relation to assembly loops or not. Isn't it
related to using fortran or not?

> I am worried about it, because it seems to effects the density of water.
Can you be more specific? Give some numbers and simulation details.

> 
> ***************************************************************
> Going to use C-settle (573 waters)
> wo = 0.888096, wh =0.0559521, wohh = 18.0154,
> rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333,
> rone = 1, dHH = 0.16333, dOH = 0.1
> ***************************************************************
> 
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From ygmu at theochem.uni-frankfurt.de  Fri Aug 22 10:34:00 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Fri Aug 22 10:34:00 2003
Subject: [gmx-users] a question
In-Reply-To: <1061538098.2073.6.camel@localhost.localdomain>
Message-ID: <Pine.LNX.4.44.0308221003440.16142-100000@marge.theochem.uni-frankfurt.de>

We have two complied versions of gromacs, one is complied by intel fortran
7.0, one is complied g77

I check different water models,

one is spc, one is tip3p amber model with  1146 water molecules in each
case (with PME cutoff 1.0)

By using the intel fortran versions

for spc such line is printed out
 ***************************************************************
 Going to use C-settle (573 waters)
 wo = 0.888096, wh =0.0559521, wohh = 18.0154,
 rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333,
 rone = 1, dHH = 0.16333, dOH = 0.1
 ***************************************************************

the average density turns out to be  966

for tip3p such line is printed out
********************************************************
Going to use C-settle (9781 waters)
wo = 0.888099, wh =0.0559503, wohh = 18.016,
rc = 0.075695, ra = 0.00655606 rb = 0.0520322, rc2 = 0.15139,
rone = 1, dHH = 0.15139, dOH = 0.09572
**********************************************************

the average density turns out to be  986
(exactly as the amber sander results)

which mean that it do simulated using different water model.


But when I use g77 version,
no "Going to use C-settle (573 waters)" line appears.
the different water model simulations nearly give the same density:
966 , which turns out that it cannot use correctly the other water model.



Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On 22 Aug 2003, David van der Spoel wrote:

> On Fri, 2003-08-22 at 09:14, Yuguang Mu wrote:
> > In the output log file in some case the following line is printed out
> > (when gromacs is compiled with assembly innerloops)
> > In other cases without assembly innerloops, this didnot print out.
> >
> This should not have any relation to assembly loops or not. Isn't it
> related to using fortran or not?
>
> > I am worried about it, because it seems to effects the density of water.
> Can you be more specific? Give some numbers and simulation details.
>
> >
> > ***************************************************************
> > Going to use C-settle (573 waters)
> > wo = 0.888096, wh =0.0559521, wohh = 18.0154,
> > rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333,
> > rone = 1, dHH = 0.16333, dOH = 0.1
> > ***************************************************************
> >
> > Dr. Yuguang Mu
> > Institute for Physical and Theoretical Chemistry
> > J.W. Goethe University Frankfurt am Main
> > Marie Curie Str. 11
> > 60439 Frankfurt/Main, Germany
> > Tel: +49-(0)69-798-29711
> >
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From aswin_biogenie at yahoo.co.uk  Fri Aug 22 10:50:01 2003
From: aswin_biogenie at yahoo.co.uk (Aswin Narain)
Date: Fri Aug 22 10:50:01 2003
Subject: [gmx-users] histidine charges
Message-ID: <20030822084843.93305.qmail@web60006.mail.yahoo.com>

hi all,
I was just wondering how the protonation states of
Histidines are 
assigned by gromacs? For some histidines with low
solvent 
accessibility (found by means of WHATIF) the
Histidines are 
assigned a protonation state of HISB (accessibility is
less than 
2.0) but for an accessibility of 24.9014 the histidine
is assigned 
a state HISB and for an accessibility of 19.305 the
histidine is 
assigned a state HISA then a histidine with
accessibility 4.1372 
the state assigned is HISH by gromacs  on what basis
is the 
assignments made as I am trying to do some pH based MD
work??

For Jayant James Jayasundar

Aswin

=====
 Aswin Sai Narain. S
Student
Centre for Biotechnology
Anna University
Chennai 25
Residence
20, 3rd main road
Nanganallur
Chennai 61



__________________________________
Do you Yahoo!?
Yahoo! Calendar - Free online calendar with sync to Outlook(TM).
http://calendar.yahoo.com


From spoel at xray.bmc.uu.se  Fri Aug 22 11:05:01 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Fri Aug 22 11:05:01 2003
Subject: [gmx-users] a question
In-Reply-To: <Pine.LNX.4.44.0308221003440.16142-100000@marge.theochem.uni-frankfurt.de>
References: 	 <Pine.LNX.4.44.0308221003440.16142-100000@marge.theochem.uni-frankfurt.de>
Message-ID: <1061542862.2073.21.camel@localhost.localdomain>

On Fri, 2003-08-22 at 10:32, Yuguang Mu wrote:
> We have two complied versions of gromacs, one is complied by intel fortran
> 7.0, one is complied g77
> 
> I check different water models,
> 
> one is spc, one is tip3p amber model with  1146 water molecules in each
> case (with PME cutoff 1.0)
> 
> By using the intel fortran versions
> 
> for spc such line is printed out
>  ***************************************************************
>  Going to use C-settle (573 waters)
>  wo = 0.888096, wh =0.0559521, wohh = 18.0154,
>  rc = 0.081665, ra = 0.00645837 rb = 0.051255, rc2 = 0.16333,
>  rone = 1, dHH = 0.16333, dOH = 0.1
>  ***************************************************************
> 
> the average density turns out to be  966
> 
> for tip3p such line is printed out
> ********************************************************
> Going to use C-settle (9781 waters)
> wo = 0.888099, wh =0.0559503, wohh = 18.016,
> rc = 0.075695, ra = 0.00655606 rb = 0.0520322, rc2 = 0.15139,
> rone = 1, dHH = 0.15139, dOH = 0.09572
> **********************************************************
> 
> the average density turns out to be  986
> (exactly as the amber sander results)
In both case above you use the C version of the routines, and you see
that the different models are represented correctly and hence you get
the correct results.


> 
> which mean that it do simulated using different water model.
> 
> 
> But when I use g77 version,
> no "Going to use C-settle (573 waters)" line appears.
> the different water model simulations nearly give the same density:
> 966 , which turns out that it cannot use correctly the other water model.
Now when you use the fortran version no such information is printed, but
it should still work. 

Could you specify how you compiled the programs?
(configure command + environment variables + make command).

On x86 architecture it does not make sense to use fortran (except,
maybe, when using double precision on Pentium 3 or Athlon), because the
assembly loops are faster anyway. The Intel compiler should produce
slightly faster code for things like shake/settle etc.

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From jxs818 at bham.ac.uk  Fri Aug 22 12:45:01 2003
From: jxs818 at bham.ac.uk (jxs818 at bham.ac.uk)
Date: Fri Aug 22 12:45:01 2003
Subject: [gmx-users] growing ligands in binding pockets
Message-ID: <E19q9On-0005xf-00@www.bham.ac.uk>

Hi All, 
I have an occluded ligand binding site, which is located in 
a protein model. If it is possible I would like to "grow" 
the ligand in the binding pocket so that at time 0 the 
ligand binding site is 0% occupied and at time x the ligand 
binding site is 100% occupied. It sounds like FEP (i think)
but i dont know anything about this, so I thought I had 
better check before going ahead.
As usual an help will be gratefully accepted.
Cheers in advance
John  




From ubmurzyn at cyf-kr.edu.pl  Fri Aug 22 12:50:01 2003
From: ubmurzyn at cyf-kr.edu.pl (Krzysztof Murzyn)
Date: Fri Aug 22 12:50:01 2003
Subject: [gmx-users] rhombic dodecahedron membrane simulations
Message-ID: <3F45E582.3040409@cyf-kr.edu.pl>

Hi all,

I'd like to perform an MD simulation of a lipid bilayer system using 
rhombic dodecahedron periodic boundary conditions. My starting 
configuration is in a rectangular box with dimensions, say, a, b and c 
(a != b != c). I guess I should use editconf with -box A B C -angles 60 
60 60; however, to preserve box volume new box dimensions must be 
somewhat bigger (by factor 1/sin(60) or so?).

Could someone give me any tips how to convert a rectangular box into a 
rhombic dodecahedron box?

Regards,
Krzysztof




From spoel at xray.bmc.uu.se  Fri Aug 22 13:55:01 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Fri Aug 22 13:55:01 2003
Subject: [gmx-users] rhombic dodecahedron membrane simulations
In-Reply-To: <3F45E582.3040409@cyf-kr.edu.pl>
References: <3F45E582.3040409@cyf-kr.edu.pl>
Message-ID: <1061553029.2073.32.camel@localhost.localdomain>

On Fri, 2003-08-22 at 11:42, Krzysztof Murzyn wrote:
> Hi all,
> 
> I'd like to perform an MD simulation of a lipid bilayer system using 
> rhombic dodecahedron periodic boundary conditions. My starting 
> configuration is in a rectangular box with dimensions, say, a, b and c 
> (a != b != c). I guess I should use editconf with -box A B C -angles 60 
> 60 60; however, to preserve box volume new box dimensions must be 
> somewhat bigger (by factor 1/sin(60) or so?).
> 
> Could someone give me any tips how to convert a rectangular box into a 
> rhombic dodecahedron box?
> 
How about:
editconf -f spc216.gro -bt dodecahedron -o ccc.gro -box 2.1 2.1 2.1

Check that the volume remains the same (or indeed sligthly larger) and
that your lipids don't break...
 

> Regards,
> Krzysztof
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From mceruso at physbio.mssm.edu  Fri Aug 22 20:25:01 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Fri Aug 22 20:25:01 2003
Subject: [gmx-users]  OPLS C-terminal Capping of Glu residue a bug?
In-Reply-To: <03082011314000.14300@fer-net.fcq.unc.edu.ar>
Message-ID: <IGEALMIPJBHPAJBIPPJEIEDLCAAA.mceruso@physbio.mssm.edu>

Hi-
I was generating the topology for a protein with a Glu residue at the
C-terminus and I got an absurd total charge of -0.13
It appears that the charge on the C-alpha atom is the culprit. When inside
the protein the Ca of Glu is opls_224B with a charge of 0.14, at the
C-terminus pdb2gmx labels the Glu as opls_285 with a charge of -0.09.
Looking at other topologies the last residues has an opls_283 for Ca with a
charge of 0.04, which seems to be the correct charge.
Marc



From lindahl at stanford.edu  Fri Aug 22 20:38:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Fri Aug 22 20:38:01 2003
Subject: [gmx-users]  OPLS C-terminal Capping of Glu residue a bug?
In-Reply-To: <IGEALMIPJBHPAJBIPPJEIEDLCAAA.mceruso@physbio.mssm.edu>
Message-ID: <6B7157A1-D4CF-11D7-9F54-000A95A099E0@stanford.edu>

Hi Marco,

Thanks, I think we've already fixed this, but I'll check it.

You can change the charge manually in the file top/ffoplsaa-c.tdb.

Don't change the atomtype, though - GLY is special since it doesn't 
have any real sidechain.

Cheers,

Erik

On Friday, August 22, 2003, at 11:24 AM, Marco Ceruso wrote:

>
> Hi-
> I was generating the topology for a protein with a Glu residue at the
> C-terminus and I got an absurd total charge of -0.13
> It appears that the charge on the C-alpha atom is the culprit. When 
> inside
> the protein the Ca of Glu is opls_224B with a charge of 0.14, at the
> C-terminus pdb2gmx labels the Glu as opls_285 with a charge of -0.09.
> Looking at other topologies the last residues has an opls_283 for Ca 
> with a
> charge of 0.04, which seems to be the correct charge.
> Marc
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From mceruso at physbio.mssm.edu  Fri Aug 22 20:48:00 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Fri Aug 22 20:48:00 2003
Subject: [gmx-users]  OPLS C-terminal Capping of Glu residue a bug?
In-Reply-To: <6B7157A1-D4CF-11D7-9F54-000A95A099E0@stanford.edu>
Message-ID: <IGEALMIPJBHPAJBIPPJECEDMCAAA.mceruso@physbio.mssm.edu>


Hi Erik-
it was a GLU not a GLY at the C-term
marco



-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Erik Lindahl
Sent: Friday, August 22, 2003 2:36 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] OPLS C-terminal Capping of Glu residue a bug?


Hi Marco,

Thanks, I think we've already fixed this, but I'll check it.

You can change the charge manually in the file top/ffoplsaa-c.tdb.

Don't change the atomtype, though - GLY is special since it doesn't 
have any real sidechain.

Cheers,

Erik

On Friday, August 22, 2003, at 11:24 AM, Marco Ceruso wrote:

>
> Hi-
> I was generating the topology for a protein with a Glu residue at the
> C-terminus and I got an absurd total charge of -0.13
> It appears that the charge on the C-alpha atom is the culprit. When 
> inside
> the protein the Ca of Glu is opls_224B with a charge of 0.14, at the
> C-terminus pdb2gmx labels the Glu as opls_285 with a charge of -0.09.
> Looking at other topologies the last residues has an opls_283 for Ca 
> with a
> charge of 0.04, which seems to be the correct charge.
> Marc
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.




From lindahl at stanford.edu  Fri Aug 22 21:39:00 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Fri Aug 22 21:39:00 2003
Subject: [gmx-users]  OPLS C-terminal Capping of Glu residue a bug?
In-Reply-To: <IGEALMIPJBHPAJBIPPJECEDMCAAA.mceruso@physbio.mssm.edu>
Message-ID: <F9D1C03F-D4D7-11D7-9F54-000A95A099E0@stanford.edu>

Hi Marco,

Download the updated version of OPLS that I put on the site last week 
(Contributions section, IIRC) and check if the problem persists.

Cheers,

Erik


On Friday, August 22, 2003, at 11:46 AM, Marco Ceruso wrote:

>
>
> Hi Erik-
> it was a GLU not a GLY at the C-term
> marco
>
>
>
> -----Original Message-----
> From: gmx-users-admin at gromacs.org 
> [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of Erik Lindahl
> Sent: Friday, August 22, 2003 2:36 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] OPLS C-terminal Capping of Glu residue a bug?
>
>
> Hi Marco,
>
> Thanks, I think we've already fixed this, but I'll check it.
>
> You can change the charge manually in the file top/ffoplsaa-c.tdb.
>
> Don't change the atomtype, though - GLY is special since it doesn't
> have any real sidechain.
>
> Cheers,
>
> Erik
>
> On Friday, August 22, 2003, at 11:24 AM, Marco Ceruso wrote:
>
>>
>> Hi-
>> I was generating the topology for a protein with a Glu residue at the
>> C-terminus and I got an absurd total charge of -0.13
>> It appears that the charge on the C-alpha atom is the culprit. When
>> inside
>> the protein the Ca of Glu is opls_224B with a charge of 0.14, at the
>> C-terminus pdb2gmx labels the Glu as opls_285 with a charge of -0.09.
>> Looking at other topologies the last residues has an opls_283 for Ca
>> with a
>> charge of 0.04, which seems to be the correct charge.
>> Marc
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From ekeaveny at dam.brown.edu  Fri Aug 22 23:13:00 2003
From: ekeaveny at dam.brown.edu (Eric Edward Keaveny)
Date: Fri Aug 22 23:13:00 2003
Subject: [gmx-users] gromacs under cygwin
Message-ID: <Pine.LNX.4.44.0308221706010.28088-100000@fritz.dam.brown.edu>

Claudio-

I'm having the same problems with pdb2gmx.  Any luck fixing the problem?

Eric



From sinhvis2 at iit.edu  Fri Aug 22 23:48:00 2003
From: sinhvis2 at iit.edu (Vishal Kumar Sinha)
Date: Fri Aug 22 23:48:00 2003
Subject: [gmx-users] gromacs under sunMPI
Message-ID: <aa329baa8203.aa8203aa329b@iit.edu>

gmx-users:

Hi 

I am problem with the configuration of gromacs under Sun MPI on sun solaris cluster.
The error I am getting is as follow:
checking for mpicc... no
checking for mpcc... mpcc
checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with mpcc
Any Help

Regards
Vishal

IIT Chicago



From lindahl at stanford.edu  Fri Aug 22 23:57:00 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Fri Aug 22 23:57:00 2003
Subject: [gmx-users] gromacs under sunMPI
In-Reply-To: <aa329baa8203.aa8203aa329b@iit.edu>
Message-ID: <3A1D0B1B-D4EB-11D7-BD36-000A95A099E0@stanford.edu>

Check config.log for the actual error message.

You can also try specifying the normal compiler and adding 
includes/libraries yourself, as described in the frequently asked 
questions online.

Cheers,

Erik


On Friday, August 22, 2003, at 02:38 PM, Vishal Kumar Sinha wrote:

> gmx-users:
>
> Hi
>
> I am problem with the configuration of gromacs under Sun MPI on sun 
> solaris cluster.
> The error I am getting is as follow:
> checking for mpicc... no
> checking for mpcc... mpcc
> checking whether the MPI cc command works... configure: error: Cannot 
> compile and link MPI code with mpcc
> Any Help
>
> Regards
> Vishal
>
> IIT Chicago
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From cpchng at bii.a-star.edu.sg  Sat Aug 23 04:12:00 2003
From: cpchng at bii.a-star.edu.sg (cpchng at bii.a-star.edu.sg)
Date: Sat Aug 23 04:12:00 2003
Subject: [gmx-users] gromacs under sunMPI
In-Reply-To: <aa329baa8203.aa8203aa329b@iit.edu>
References: <aa329baa8203.aa8203aa329b@iit.edu>
Message-ID: <53818.202.156.211.159.1061604660.squirrel@web.bii.a-star.edu.sg>

Hi Vishal,

   I also had problems compiling Gromacs on Solaris cluster, using SUN MPI.
With the help of Chris (sorry, forgot his last name) from this user group,
I managed to get it working. However, the error I got was about C compiler
not being able to create executables.
Anyway, in addition to what Erik said, you may wish to try the following:

First, compile w/o MPI and install the binaries.

For MPI version of mdrun: (assuming SUN MPI is in /opt/SUNWhpc/ and fftw
libraries is /usr/local/include.)

export CPPFLAGS="-I/opt/SUNWhpc/include -I/usr/local/include"
export CFLAGS="-fast -xtarget=ultra3 -xarch=v8plusb -xvector"
export LDFLAGS="-fast -xtarget=ultra3 -xarch=v8plusb -xvector
-L/opt/SUNWhpc/lib -R/opt/SUNWhpc/lib -L/usr/local/lib -R/usr/local/lib"
export LIBS="-lmpi -lmopt"
export MPICC=mpcc
(else will complain that mpicc does not compile)

./configure --prefix=/usr/local/gromacs --enable-shared
--program-suffix=_mpi_d
--enable-mpi --disable-float

(See that dfftw has been used.)

make mdrun (rest of tools not affected by MPI)
make install-mdrun

Hope this works for you.

cheers,
choon-peng
-------
Research Associate
Bioinformatics Institute, Singapore

> gmx-users:
>
> Hi
>
> I am problem with the configuration of gromacs under Sun MPI on sun
> solaris cluster. The error I am getting is as follow:
> checking for mpicc... no
> checking for mpcc... mpcc
> checking whether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with mpcc Any Help
>
> Regards
> Vishal
>
> IIT Chicago
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.




From taeho.kim at utoronto.ca  Sun Aug 24 05:09:01 2003
From: taeho.kim at utoronto.ca (taeho.kim at utoronto.ca)
Date: Sun Aug 24 05:09:01 2003
Subject: [gmx-users]  OPLS C-terminal Capping of Glu residue a bug?
Message-ID: <1061694431.3f482bdfe5870@webmail.utoronto.ca>

Hi, Erik

I am just wondering whether Gromacs performance on Opteron has been 
optimized.

1. yes, then do I need to use a special option for compilation.
2. no, I hope it happen before this Christmas.

If I do some BM on Opteron with Gromacs 3.1.5_pre1, it seems to me the data 
is useful for just comparison(before/after optimizaton), not reliable to 
evaluate Opteron as decision making data. 

Thanks,

taeho


From lindahl at stanford.edu  Sun Aug 24 05:55:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Sun Aug 24 05:55:01 2003
Subject: [gmx-users]  OPLS C-terminal Capping of Glu residue a bug?
In-Reply-To: <1061694431.3f482bdfe5870@webmail.utoronto.ca>
Message-ID: <73527424-D5E6-11D7-8A48-000A95A099E0@stanford.edu>

Hi,

Short answer: Just compile in 32-bit mode and the Opteron performance 
will be excellent (using SSE assembly loops).

Long answer: The current gromacs version doesn't have any 64-bit 
opteron assembly loops, but I have very strong reasons to believe 
future versions will be (read: I have already written the x86-64 
assembly loops :-). In practice they won't be any faster than the 
32-bit loops, and in some cases it might actually be slower due to the 
64-bit pointers. This doesn't mean the 64-bit mode is bad, it is just 
because the AMD chip is really excellent at running the 32-bit assembly 
code! (and it is in agreement with other x86-64 benchmarks). Future 
generations of x86-64 might be more focused on 64-bit performance 
though, so it might matter in a generation or two, and they 64-bit 
loops will make it easier to get good performance on huge systems 
(millions or billions of particles).


Just make sure you use 32-bit mode, and that the log file says 
something about SSE (so you are not running 64-bit without assembly 
loops).

Cheers,

Erik

> Hi, Erik
>
> I am just wondering whether Gromacs performance on Opteron has been
> optimized.
>
> 1. yes, then do I need to use a special option for compilation.
> 2. no, I hope it happen before this Christmas.
>
> If I do some BM on Opteron with Gromacs 3.1.5_pre1, it seems to me the 
> data
> is useful for just comparison(before/after optimizaton), not reliable 
> to
> evaluate Opteron as decision making data.
>
> Thanks,
>
> taeho
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From malcolm.b.gillies at anu.edu.au  Mon Aug 25 08:43:01 2003
From: malcolm.b.gillies at anu.edu.au (Malcolm Gillies)
Date: Mon Aug 25 08:43:01 2003
Subject: [gmx-users] mdrun crash when -np 8, not when -np 4
In-Reply-To: <1061534920.2073.1.camel@localhost.localdomain>
References: <1061519712.24599.16.camel@bakunin>
	 <1061534920.2073.1.camel@localhost.localdomain>
Message-ID: <1061793735.8624.36.camel@bakunin>

On Fri, 2003-08-22 at 16:48, David van der Spoel wrote:
> On Fri, 2003-08-22 at 04:35, Malcolm Gillies wrote:
> > I have an mdrun job which crashes when I attempt to run it over 8
> > processors, but which appears to run fine with 4 processors. Any
> > suggestions?
> Could it be that you have no water left on processor 0 (which is where I
> presume that the problem occurs)?
> 
> This is a known bug, which has not been resolved completely yet.

Indeed, there are no water molecules left on processor 0:

    There are 0 optimized solvent molecules on node 0
    There are 0 optimized water molecules on node 0

Is there a workaround for this problem?

cheers,

Malcolm



From feenstra at chem.vu.nl  Mon Aug 25 08:49:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug 25 08:49:01 2003
Subject: [gmx-users] growing ligands in binding pockets
In-Reply-To: <E19q9On-0005xf-00@www.bham.ac.uk>
References: <E19q9On-0005xf-00@www.bham.ac.uk>
Message-ID: <3F464049.6090607@chem.vu.nl>

jxs818 at bham.ac.uk wrote:
> Hi All, 
> I have an occluded ligand binding site, which is located in 
> a protein model. If it is possible I would like to "grow" 
> the ligand in the binding pocket so that at time 0 the 
> ligand binding site is 0% occupied and at time x the ligand 
> binding site is 100% occupied. It sounds like FEP (i think)
> but i dont know anything about this, so I thought I had 
> better check before going ahead.

Yep, that is FEP. You'll also need 'soft-core' potentials, I'm not sure
if they were already implemented in the lastest release version.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From feenstra at chem.vu.nl  Mon Aug 25 08:49:03 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Mon Aug 25 08:49:03 2003
Subject: [gmx-users] histidine charges
In-Reply-To: <20030822084843.93305.qmail@web60006.mail.yahoo.com>
References: <20030822084843.93305.qmail@web60006.mail.yahoo.com>
Message-ID: <3F4641C1.8050802@chem.vu.nl>

Aswin Narain wrote:
> hi all,
> I was just wondering how the protonation states of Histidines are 
> assigned by gromacs? For some histidines with low solvent 
> accessibility (found by means of WHATIF) the Histidines are 
> assigned a protonation state of HISB (accessibility is less than 
> 2.0) but for an accessibility of 24.9014 the histidine is assigned 
> a state HISB and for an accessibility of 19.305 the histidine is 
> assigned a state HISA then a histidine with accessibility 4.1372 
> the state assigned is HISH by gromacs  on what basis is the 
> assignments made as I am trying to do some pH based MD work??

pdb2gmx determines (guesses) at protonation state by examining
possible hydrogen bonding partners. I'm not sure how much it
actually prints out about it's decisions. Non-accessible residues
will be (almost) completely determined by the possible H-bonding
partners, also interior but accessible residues can be influenced
greatly by their surrounding, and only accessible ones depend wholly
on solvent pH.

There was some extended discussion on the list on pH-MD a week or so ago.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From malcolm.b.gillies at anu.edu.au  Mon Aug 25 08:54:01 2003
From: malcolm.b.gillies at anu.edu.au (Malcolm Gillies)
Date: Mon Aug 25 08:54:01 2003
Subject: [gmx-users] appropriate coupling constants for extended systems
Message-ID: <1061794387.8624.48.camel@bakunin>

Hi,

I'm wondering if anyone can give me some rules of thumb, wise words,
and/or literature references, on choosing coupling constants for
Nose-Hoover and Parrinello-Rahman extended system schemes. Frenkel and
Smit isn't helping me much here. At the moment, for an NPT simulation, I
have something like:

    ; Nose-Hoover coupling is on in two groups
    Tcoupl              =  Nose-Hoover
    tau_t               =  0.1      0.1
    tc-grps             =  protein  sol
    ref_t               =  300      300
    ; Pressure coupling is on
    Pcoupl              =  Parrinello-Rahman
    Pcoupltype          =  isotropic
    tau_p               =  0.5
    compressibility     =  4.5e-5
    ref_p               =  1.0

cheers,

Malcolm
--
Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
John Curtin School of Medical Research, Australian National University



From spoel at xray.bmc.uu.se  Mon Aug 25 09:17:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Mon Aug 25 09:17:01 2003
Subject: [gmx-users] mdrun crash when -np 8, not when -np 4
In-Reply-To: <1061793735.8624.36.camel@bakunin>
References: <1061519712.24599.16.camel@bakunin>
	 <1061534920.2073.1.camel@localhost.localdomain>
	 <1061793735.8624.36.camel@bakunin>
Message-ID: <1061796136.1737.17.camel@h28n2fls34o1123.telia.com>

On Mon, 2003-08-25 at 08:42, Malcolm Gillies wrote:
> On Fri, 2003-08-22 at 16:48, David van der Spoel wrote:
> > On Fri, 2003-08-22 at 04:35, Malcolm Gillies wrote:
> > > I have an mdrun job which crashes when I attempt to run it over 8
> > > processors, but which appears to run fine with 4 processors. Any
> > > suggestions?
> > Could it be that you have no water left on processor 0 (which is where I
> > presume that the problem occurs)?
> > 
> > This is a known bug, which has not been resolved completely yet.
> 
> Indeed, there are no water molecules left on processor 0:
> 
>     There are 0 optimized solvent molecules on node 0
>     There are 0 optimized water molecules on node 0
> 
> Is there a workaround for this problem?
Apart from reducing the number of processors, no.
> 
> cheers,
> 
> Malcolm
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From periole at inka.mssm.edu  Mon Aug 25 19:18:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Mon Aug 25 19:18:01 2003
Subject: [gmx-users] growing ligands in binding pockets
References: <E19q9On-0005xf-00@www.bham.ac.uk>
Message-ID: <005a01c36b2c$aa72d010$d83a4a86@fox>

Hello John,

Remember that the apparition/disparition of your ligand is supposed
to only be a perturbation to your system. This is a necessary condition
for your FEP calculation to be valid. That is why people use a lambda
to decompose the "transformation" into perturbations as small as possible
within the computer feasability.
People have done that for cations alchmistry (good results), or some
mutation studies (not sure it works for all kind of mutants), ligand I don't
know. I am just trying to stress out the bigger the perturbation the less
accurate the result !!


XAvier





From tccf at epq.ime.eb.br  Mon Aug 25 19:22:01 2003
From: tccf at epq.ime.eb.br (Tanos)
Date: Mon Aug 25 19:22:01 2003
Subject: [gmx-users] trjconv
Message-ID: <3F4A4572.1040506@epq.ime.eb.br>

	Hi folks,
	I have finished a MD simulation on a protein in a water box and now I 
need to eliminate the water molecules from the .gro file in order to 
perform the conformational analysis of the protein after MD. I am trying 
to do this using trjconv but I am not having any success. Could someone 
say me the right order of comands to use to eliminate the water 
molecules and create a new .gro file having just the coordinates of the 
the protein after MD ???? The information about this, from the manual, 
is not clear for me.
	I am typing "trjconv -f 'filename.gro' -o 'newfilename'.gro" What am I 
doing wrong ????????
	Thanks in advance.
	Tanos Celmar Costa Franca.
	IME - Rio de Janeiro - Brazil



From periole at inka.mssm.edu  Mon Aug 25 19:33:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Mon Aug 25 19:33:01 2003
Subject: [gmx-users] trjconv
References: <3F4A4572.1040506@epq.ime.eb.br>
Message-ID: <006601c36b2e$c63e38a0$d83a4a86@fox>


You have to create an index with the protein (in the default index):

make_ndx -f conf-protein 

generates index.ndx 

after that you do

trajconv -f traj.xtc -n index.ndx -o traj-prot.xtc 

the program asks you what you want in the output traj 

XAvier




From mceruso at physbio.mssm.edu  Mon Aug 25 19:33:02 2003
From: mceruso at physbio.mssm.edu (Marco Ceruso)
Date: Mon Aug 25 19:33:02 2003
Subject: [gmx-users] trjconv
In-Reply-To: <3F4A4572.1040506@epq.ime.eb.br>
Message-ID: <IGEALMIPJBHPAJBIPPJEEEECCAAA.mceruso@physbio.mssm.edu>

hi-
create an index.ndx file with mkae_ndx
then trjconv f traj.xtc -o prot.xtc -n index.ndx
this will prompt trjconv to read the index file and ask you which group you
want for output "Protein" in your case.
this will create prot.xtc a trajectory with the protein only
Marco


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Tanos
Sent: Monday, August 25, 2003 1:21 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] trjconv


	Hi folks,
	I have finished a MD simulation on a protein in a water box and now I
need to eliminate the water molecules from the .gro file in order to
perform the conformational analysis of the protein after MD. I am trying
to do this using trjconv but I am not having any success. Could someone
say me the right order of comands to use to eliminate the water
molecules and create a new .gro file having just the coordinates of the
the protein after MD ???? The information about this, from the manual,
is not clear for me.
	I am typing "trjconv -f 'filename.gro' -o 'newfilename'.gro" What am I
doing wrong ????????
	Thanks in advance.
	Tanos Celmar Costa Franca.
	IME - Rio de Janeiro - Brazil

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.




From Feenstra at chem.vu.nl  Tue Aug 26 10:57:01 2003
From: Feenstra at chem.vu.nl (K.A. Feenstra)
Date: Tue Aug 26 10:57:01 2003
Subject: [gmx-users] Re: GROMACS question
In-Reply-To: <5.2.1.1.0.20030825165349.01ad7ae0@pop3.norton.antivirus>
References: <5.2.1.1.0.20030825165349.01ad7ae0@pop3.norton.antivirus>
Message-ID: <3F4B213C.9010603@chem.vu.nl>

J.Raul Grigera wrote:
> Dear Anton,
>          I am trying to produce a simulation with a 'non -existing' 
> atoms.  When producing the .gro files trough editconf I can not tell  
> him  the van der Waals radius.  Using the option -vdwd 2.5 (is a big 
> atom!) always assign the default value.  Can you help me?

I'm not sure what you are trying to do. Could you explain in more detail?
Furthermore, please direct your question to the Gromacs users mailing list
(gmx-users at gromacs.org, subscribe at the website www.gromacs.org).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|



From swetha at www.cdfd.org.in  Tue Aug 26 13:50:01 2003
From: swetha at www.cdfd.org.in (Swetha Vijayakrishan)
Date: Tue Aug 26 13:50:01 2003
Subject: [gmx-users] D-L conversion!
Message-ID: <Pine.SGI.4.44.0308261719460.145445-100000@www.cdfd.org.in>

hi all,

I had run a 2 nanosecond MD using Charmm.
Now i find a few of the residues having their chirality changed from L to
D especially the Prolines.
Is this very common in MD? Or have i made some mistake.
Does anybody know how i can rectify this problem without rerunning the MD
again??

thanks

swetha









*******************************************************************************


Swetha Vijayakrishnan

Project Assistant
C/O Dr.Shekhar.C.Mande
Centre for DNA Fingerprinting and Diagnostics(CDFD),
ECIL Road,Nacharam,
Hyderabad - 500076

Phone:: Direct: 91-040-7171442
        Indirect: 91-040-7151344/46/47/56 (lab extn 1400)

Fax  :: 91-040-(7155479-7155610>

Email:: swetha at cdfd.org.in
        swethasenorita at yahoo.com




From kwoods at stanford.edu  Tue Aug 26 18:23:01 2003
From: kwoods at stanford.edu (Kristina Nicole Woods)
Date: Tue Aug 26 18:23:01 2003
Subject: [gmx-users] the nucleotide thymine (THY) in gromacs
Message-ID: <Pine.GSO.4.44.0308260916580.19393-100000@myth8.Stanford.EDU>

Hello,

I couldn't find the nucleotide thymine (THY) in the ff*.rtp files.  I did
find DTHY though.  Does it exist somewhere and I missed it?

In using pdb2gmx on an DNA pdb file, it mapped THF for THY in my
file...and that's not really what I'm looking for.

Thank you,

Kristina :)





From tccf at epq.ime.eb.br  Tue Aug 26 20:21:02 2003
From: tccf at epq.ime.eb.br (Tanos)
Date: Tue Aug 26 20:21:02 2003
Subject: [gmx-users] trjconv again
Message-ID: <3F4BA4E1.4090701@epq.ime.eb.br>

Dears
Xavier Periole and Marco Ceruso,
Thank you very much for your help with trjconv. It worked very well with 
  files .xtc .ndx and .gro etc...But, unfortunatelly, the file generated 
brings all the frames of the dynamics. What I want is just the last 
frame. /i tryed the flag -e (last frame to read from trajectory) of the 
manual but it didn't worked Do you know how to apply the flag -e in the 
outputed file .gro from a dynamics to have only the last frame in a .gro 
file ??????
Thanks in advance.
Tanos Franca.



From periole at inka.mssm.edu  Tue Aug 26 20:29:01 2003
From: periole at inka.mssm.edu (Xavier Periole)
Date: Tue Aug 26 20:29:01 2003
Subject: [gmx-users] trjconv again
References: <3F4BA4E1.4090701@epq.ime.eb.br>
Message-ID: <005b01c36bff$caf19b90$d83a4a86@fox>


Two solutions :

1) you still want to go through the trajectory and you actually have to
give the value of the last frame, e.g., -e 2000 (2ns if saved every 1 ps)
and put -o conf-200.gro instead of -o traj,xtc
2) you should have a file called confout.gro, which is the final
conformation
of your system, at the end of the simulation. You can make a :
editconf -f confout.gro -n index (same as before) -o only_protein.gro

XAvier





From albert_sun9 at yahoo.com  Tue Aug 26 23:33:01 2003
From: albert_sun9 at yahoo.com (Albert Sun)
Date: Tue Aug 26 23:33:01 2003
Subject: [gmx-users] ngmx:  Segmentation fault 
In-Reply-To: <005b01c36bff$caf19b90$d83a4a86@fox>
Message-ID: <20030826213231.49714.qmail@web21508.mail.yahoo.com>


Dear Users,

When I ran ngmx, it had error:  

" 

 Reading file pul1.tpr, VERSION 3.1.2 (single precision)

trn version: GMX_trn_file

Reading frame 0 time 0.000 Opening library file /usr/local/gromacs/share/top/aminoacids.dat

Opening library file /usr/local/gromacs/share/top/export.dlg

Opening library file /usr/local/gromacs/share/top/bonds.dlg

Segmentation fault      "
Could you advise me how to solve the problem?
 
Thanks!
 
Albert

 



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From spoel at xray.bmc.uu.se  Wed Aug 27 09:01:01 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Wed Aug 27 09:01:01 2003
Subject: [gmx-users] ngmx:  Segmentation fault
In-Reply-To: <20030826213231.49714.qmail@web21508.mail.yahoo.com>
References: <20030826213231.49714.qmail@web21508.mail.yahoo.com>
Message-ID: <1061971025.5184.6.camel@werkman.bmc.uu.se>

On Tue, 2003-08-26 at 23:32, Albert Sun wrote:
> Dear Users,
> 
> When I ran ngmx, it had error:  
> 

you give very little information. Could it be that the tpr does not
match the trajectory (in particular the tpr has not the same number of
atoms as the traj)

> " 
> 
>  Reading file pul1.tpr, VERSION 3.1.2 (single precision)
> 
> trn version: GMX_trn_file
> 
> Reading frame 0 time 0.000 Opening library file
> /usr/local/gromacs/share/top/aminoacids.dat
> 
> Opening library file /usr/local/gromacs/share/top/export.dlg
> 
> Opening library file /usr/local/gromacs/share/top/bonds.dlg
> 
> Segmentation fault      "
> 
> 
> Could you advise me how to solve the problem?
>  
> Thanks!
>  
> Albert
>  
> 
> 
> ______________________________________________________________________
> Do you Yahoo!?
> Yahoo! SiteBuilder - Free, easy-to-use web site design software
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From spoel at xray.bmc.uu.se  Wed Aug 27 09:02:01 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Wed Aug 27 09:02:01 2003
Subject: [gmx-users] D-L conversion!
In-Reply-To: <Pine.SGI.4.44.0308261719460.145445-100000@www.cdfd.org.in>
References: <Pine.SGI.4.44.0308261719460.145445-100000@www.cdfd.org.in>
Message-ID: <1061971112.5184.9.camel@werkman.bmc.uu.se>

On Wed, 2003-08-27 at 02:22, Swetha Vijayakrishan wrote:
> hi all,
> 
> I had run a 2 nanosecond MD using Charmm.
> Now i find a few of the residues having their chirality changed from L to
> D especially the Prolines.
> Is this very common in MD? Or have i made some mistake.
> Does anybody know how i can rectify this problem without rerunning the MD
> again??
No, if your protein is in a wrong conformation than you should rerun the
simulation. In this case you want to check whether there is an improper
dihedral on the Ca in the Prolines.

> 
> thanks
> 
> swetha
> 
> 
> 
> 
> 
> 
> 
> 
> 
> *******************************************************************************
> 
> 
> Swetha Vijayakrishnan
> 
> Project Assistant
> C/O Dr.Shekhar.C.Mande
> Centre for DNA Fingerprinting and Diagnostics(CDFD),
> ECIL Road,Nacharam,
> Hyderabad - 500076
> 
> Phone:: Direct: 91-040-7171442
>         Indirect: 91-040-7151344/46/47/56 (lab extn 1400)
> 
> Fax  :: 91-040-(7155479-7155610>
> 
> Email:: swetha at cdfd.org.in
>         swethasenorita at yahoo.com
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From ygmu at theochem.uni-frankfurt.de  Wed Aug 27 11:00:00 2003
From: ygmu at theochem.uni-frankfurt.de (Yuguang Mu)
Date: Wed Aug 27 11:00:00 2003
Subject: [gmx-users] doubel precision
In-Reply-To: <3F44EBE4.5A09F418@gwdg.de>
Message-ID: <Pine.LNX.4.44.0308271043380.8729-100000@marge.theochem.uni-frankfurt.de>

Whem I compiled double precision of 3.1.4, it seems work,
it has such printing:

Testing x86 processor CPUID...

Testing x86 SSE2 capabilities...
No SSE2 support found for this CPU.

In this case, it is better to recompile the program switch off the
assembly loop and enable fortran ?
by
--disable-x86-asm --enable-fortran


Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711

On Thu, 21 Aug 2003, Bert de Groot wrote:

> Dear all,
>
> we're about to renew our cluster and I'd like to share our thoughts, and
> would very much appreciate if you could share your experience/thoughts too.
> There have been some posts on this list about this issue, but there have
> been some hardware developments since then, so I figured it would make sense
> to post once again.
>
> So far we've been very happy with our dual athlons (apart from a few stability
> issues), but scaling is not that great, especially with PME. We have a few nodes
> with myrinet, but even there most jobs run on maximally 2 dual nodes
> (4 processors), because beyond that the scaling simply breaks. We've also
> played with gigabit ethernet and the M-VIA protocol, but these only yield
> marginal improvements, especially on the faster nodes.
>
> Some points that we considered are:
> -the latest generation of SCALI cards seem to have a quite promising
>  price/performance ratio. Does anyone have recent experience with SCALI?
> -what about quad Xeon boards?
> -any alternative to scali or myrinet for improved low latency networking?
> -can we expect developments in gromacs in the near future that will
>  reduce the network load/improve scaling? (I don't want to push the developers
>  here, they're doing a splendid job. It's only to optimise the planning).
>
>
> cheers,
>
> Bert
>
> ____________________________________________________________________________
> Dr. Bert de Groot
>
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> 37077 Goettingen, Germany
>
> tel: +49-551-2011306, fax: +49-551-2011089
>
> email: bgroot at gwdg.de
> http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
> ____________________________________________________________________________
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>



From spoel at xray.bmc.uu.se  Wed Aug 27 11:20:02 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Wed Aug 27 11:20:02 2003
Subject: [gmx-users] doubel precision
In-Reply-To: <Pine.LNX.4.44.0308271043380.8729-100000@marge.theochem.uni-frankfurt.de>
References: 	 <Pine.LNX.4.44.0308271043380.8729-100000@marge.theochem.uni-frankfurt.de>
Message-ID: <1061979346.5184.11.camel@werkman.bmc.uu.se>

On Wed, 2003-08-27 at 10:58, Yuguang Mu wrote:
> Whem I compiled double precision of 3.1.4, it seems work,
> it has such printing:
> 
> Testing x86 processor CPUID...
> 
> Testing x86 SSE2 capabilities...
> No SSE2 support found for this CPU.
> 
> In this case, it is better to recompile the program switch off the
> assembly loop and enable fortran ?
> by
> --disable-x86-asm --enable-fortran

The proof of the pudding is in the eating...
If you have a good fortran compiler it will help, but g77 won't improve
on gcc code.

> 
> 
> Dr. Yuguang Mu
> Institute for Physical and Theoretical Chemistry
> J.W. Goethe University Frankfurt am Main
> Marie Curie Str. 11
> 60439 Frankfurt/Main, Germany
> Tel: +49-(0)69-798-29711
> 
> On Thu, 21 Aug 2003, Bert de Groot wrote:
> 
> > Dear all,
> >
> > we're about to renew our cluster and I'd like to share our thoughts, and
> > would very much appreciate if you could share your experience/thoughts too.
> > There have been some posts on this list about this issue, but there have
> > been some hardware developments since then, so I figured it would make sense
> > to post once again.
> >
> > So far we've been very happy with our dual athlons (apart from a few stability
> > issues), but scaling is not that great, especially with PME. We have a few nodes
> > with myrinet, but even there most jobs run on maximally 2 dual nodes
> > (4 processors), because beyond that the scaling simply breaks. We've also
> > played with gigabit ethernet and the M-VIA protocol, but these only yield
> > marginal improvements, especially on the faster nodes.
> >
> > Some points that we considered are:
> > -the latest generation of SCALI cards seem to have a quite promising
> >  price/performance ratio. Does anyone have recent experience with SCALI?
> > -what about quad Xeon boards?
> > -any alternative to scali or myrinet for improved low latency networking?
> > -can we expect developments in gromacs in the near future that will
> >  reduce the network load/improve scaling? (I don't want to push the developers
> >  here, they're doing a splendid job. It's only to optimise the planning).
> >
> >
> > cheers,
> >
> > Bert
> >
> > ____________________________________________________________________________
> > Dr. Bert de Groot
> >
> > Max Planck Institute for Biophysical Chemistry
> > Computational biomolecular dynamics group
> > Am Fassberg 11
> > 37077 Goettingen, Germany
> >
> > tel: +49-551-2011306, fax: +49-551-2011089
> >
> > email: bgroot at gwdg.de
> > http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
> > ____________________________________________________________________________
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From Vojtech.Spiwok at vscht.cz  Wed Aug 27 12:30:01 2003
From: Vojtech.Spiwok at vscht.cz (=?iso-8859-2?Q?Ing._Vojt=ECch_Spiwok?=)
Date: Wed Aug 27 12:30:01 2003
Subject: [gmx-users] Re: D-L conversion! (Swetha Vijayakrishan)
References: <20030827100001.24375.20759.Mailman@hawk.theophys.kth.se>
Message-ID: <023501c36c86$027d2800$39782193@vscht.cz>

> I had run a 2 nanosecond MD using Charmm.
> Now i find a few of the residues having their chirality changed from L to
> D especially the Prolines.
> Is this very common in MD? Or have i made some mistake.
> Does anybody know how i can rectify this problem without rerunning the MD
> again??
>
> thanks
>
> swetha

Charmm (as well as Gromacs) does contain improper dihedrals to maintain
correct chiralities.
"Racemization" is definitely a misatke if you want to realistically simulate
dynamics
itself but if you want to predict a structure (eg. by running
high-temperature MD
with NMR-derived restraints, simulated annealing etc.) you can change
chiralities
in final structure by some programs (I think Sybyl or Insight) and than
continue
with optimization and evaluation.

Vojtech Spiwok
ICT Prague



From gianfranco.bocchinfuso at uniroma2.it  Wed Aug 27 14:06:01 2003
From: gianfranco.bocchinfuso at uniroma2.it (Gianfranco Bocchinfuso)
Date: Wed Aug 27 14:06:01 2003
Subject: [gmx-users] 1-4 terms in Amber-Gmx traslate
Message-ID: <001301c36c93$708284a0$8e1e50a0@bocchinfuso2>

Hi all
When I translate AMBER parameters in GROMACS using for dihedrals the RB function I have to put the 1-4 terms in the [exclusion] section or I have to assign some value to this terms?
thanks
Gianfranco
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From ekeaveny at dam.brown.edu  Wed Aug 27 20:38:01 2003
From: ekeaveny at dam.brown.edu (Eric Edward Keaveny)
Date: Wed Aug 27 20:38:01 2003
Subject: [gmx-users] Seg Fault during pdb2gmx in demo
Message-ID: <Pine.LNX.4.44.0308271358230.5977-100000@fritz.dam.brown.edu>

Hi,

To start, I'm using gromacs-3.1.4 with cygwin-1.3.22-1 and gcc-3.2-3.

I've been getting a seg-fault when trying to run the demo.

Here are the last 5 lines of the pdb2gmx "pop up window" output:

-posrefc	real  1000 Force constant for position restraints
-dummy   	enum  none Convert atoms to dummy atoms: none, hydrogens 
			   or aromatics
-[no]heavyh	bool  no   Make hydrogen atoms heavy
-[no]deuterate  bool  no   Change the mass of hydrogen to 2 amu

In the demo run window I get:

Press <enter>
Starting pdb2gmx
[1] 3452
Segmentation fault (core dumped)
pdb2gmx finished
Press <enter>

And finally, the contents of the pdb2gmx.exe.stackdump file:

Exception: STATUS_ACCESS_VIOLATION at eip=004572EA

eax=20312020 ebx=002263BC ecx=00000000 edx=002263BC esi=002263C2 
edi=00455688

ebp=100304F4 esp=00225390 
program=C:\cygwin\usr\local\gromacs\i686-pc-cygwin\bin\pdb2gmx.exe

cs=001B ds=0023 es=0023 fs=0038 gs=0000 ss=0023

Stack trace:

Frame     Function  Args

100304F4  004572EA  (00000000, 00030484, 100315F8, 00000400)

10031649  000003AF  (20322020, 20414320, 53594C20, 20202020)

      5 [main] pdb2gmx 616 handle_exceptions: Error while dumping state 
(probably corrupted stack)

Anyone have any ideas or suggestions as to how to fix this problem?

Eric



From feenstra at chem.vu.nl  Thu Aug 28 08:54:01 2003
From: feenstra at chem.vu.nl (Anton Feenstra)
Date: Thu Aug 28 08:54:01 2003
Subject: [gmx-users] D-L conversion!
In-Reply-To: <Pine.SGI.4.44.0308261719460.145445-100000@www.cdfd.org.in>
References: <Pine.SGI.4.44.0308261719460.145445-100000@www.cdfd.org.in>
Message-ID: <3F4B8082.8030004@chem.vu.nl>

Swetha Vijayakrishan wrote:
> hi all,
> 
> I had run a 2 nanosecond MD using Charmm.
> Now i find a few of the residues having their chirality changed from L to
> D especially the Prolines.
> Is this very common in MD? Or have i made some mistake.
> Does anybody know how i can rectify this problem without rerunning the MD
> again??

One could argue whether doing MD with Charmm is a mistake ;-)

I would not expect L-D transitions in Prolines, these are known to be very
slow (experimentally, that is) and can be e.g. rate limiting for folding.
Don't know about the parameterization of the Charmm forcefield, however.

As for re-running, I know from other people that Charmm can be about 10
times slower than Amber, and I know from own experience that Gromacs can
be about 5-10 times faster than Amber. You do the maths...
We have a choice variety of forcefields: Gromos, OPLS (and Amber coming).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|




From spoel at xray.bmc.uu.se  Thu Aug 28 13:14:02 2003
From: spoel at xray.bmc.uu.se (David van der Spoel)
Date: Thu Aug 28 13:14:02 2003
Subject: [gmx-users] Re: [gmx-developers] RE: gmx-developers digest, Vol 1 #214 - 3 msgs
In-Reply-To: <000001c36d54$d0def920$e509ad83@CVRAMAN>
References: <000001c36d54$d0def920$e509ad83@CVRAMAN>
Message-ID: <1062072646.8154.23.camel@werkman.bmc.uu.se>

On Thu, 2003-08-28 at 13:09, Lakshmi Padmavathi wrote:
> Dear gromacs develepors,
> 
> I wopuld like to use bacterio chlorophyll in my simulations. So I would
> like to create an itp file (as building block). 
> 
> How can I know the charges and charge groups?
> 
> How can I know the improper dihedrals.
> 
> I will be very much thankful to you for answering my questions.
> 
this is more of a gmx-users question. I'll forward the result there.

Is this covalently linked to the protein? If not you can use the prodrg
server to make a topology. Otherwise you have to make an rtp entry.
Charges you have to generate yourself in some way.

> Thank you
> 
> Best regards,
> Lakshmi
> 
> 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



From Vojtech.Spiwok at vscht.cz  Thu Aug 28 15:38:01 2003
From: Vojtech.Spiwok at vscht.cz (=?iso-8859-2?Q?Ing._Vojt=ECch_Spiwok?=)
Date: Thu Aug 28 15:38:01 2003
Subject: [gmx-users] D-L conversion!
References: <20030828100002.9232.17234.Mailman@hawk.theophys.kth.se>
Message-ID: <005a01c36d69$6cf783e0$39782193@vscht.cz>

> Swetha Vijayakrishan wrote:
> > hi all,
> >
> > I had run a 2 nanosecond MD using Charmm.
> > Now i find a few of the residues having their chirality changed from L
to
> > D especially the Prolines.
> > Is this very common in MD? Or have i made some mistake.
> > Does anybody know how i can rectify this problem without rerunning the
MD
> > again??
>
> One could argue whether doing MD with Charmm is a mistake ;-)
>
> I would not expect L-D transitions in Prolines, these are known to be very
> slow (experimentally, that is) and can be e.g. rate limiting for folding.
> Don't know about the parameterization of the Charmm forcefield, however.
>
> As for re-running, I know from other people that Charmm can be about 10
> times slower than Amber, and I know from own experience that Gromacs can
> be about 5-10 times faster than Amber. You do the maths...
> We have a choice variety of forcefields: Gromos, OPLS (and Amber coming).
>
>
> --
> Groetjes,
>
> Anton

Level of D-aminoacids in dental proteins could be used for estimation of age
of corpses
(eg.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_ui
ds=8690325&dopt=Abstract)
as it raises with age, so nothing for molecular dynamics (even with Gromacs
:-)
As I know in vivo L-D transition is two-step covalent reaction, anyway.


Vojtech Spiwok
ICT Prague



From jxs818 at bham.ac.uk  Thu Aug 28 15:55:01 2003
From: jxs818 at bham.ac.uk (jxs818 at bham.ac.uk)
Date: Thu Aug 28 15:55:01 2003
Subject: [gmx-users] bond angle constraints
Message-ID: <E19sNEF-0004Zd-00@www.bham.ac.uk>

Hi all, 
I am a bit stuck. I have a protein in a ground/unactivated 
state and I also have some distance restraints from spin 
labelling with a ligand bound. I think that the overall 
secondary structure in my protein is maintained but there 
is some movement of helices etc. Can I break my protein 
down into its component secondary structural elements, then 
add constraints = all-angles (keeping these secondary 
structural elements as rigid bodies ?), then finally add 
distance restraints to parts of my protein to mimic a 
translation from the ground state to the ligand bound state.
This is probally really not right, has anyone else had a 
similiar problem??
As always any help is gratefully accepted.
John 




From alan at lac.inpe.br  Thu Aug 28 18:06:01 2003
From: alan at lac.inpe.br (Alan Wilter Sousa da Silva)
Date: Thu Aug 28 18:06:01 2003
Subject: [gmx-users] about PETA
Message-ID: <Pine.LNX.4.53.0308281302170.5145@adastra.nucleo.inpe.br>

I found out it in Web,

http://www.peta.co.jp/

What GMX guys may say about it?

It looks like quite interesting.

Cheers, 

--------------------------
Alan Wilter Sousa da Silva
--------------------------
M.Sc - Dep. F?sica - PUC/RJ
D.Sc - IBCCF/UFRJ
Bolsista Pesquisador LAC-INPE
S?o Jos? dos Campos (SP), Brasil
www.lac.inpe.br/~alan


From paloureiro at biof.ufrj.br  Thu Aug 28 20:38:01 2003
From: paloureiro at biof.ufrj.br (Pedro Alexandre Lapido Loureiro)
Date: Thu Aug 28 20:38:01 2003
Subject: [gmx-users] 1-4 interactions
Message-ID: <1062095503.3f4e4a8fc143e@webmail.biof.ufrj.br>

Dear GMX users,

I am implementing a lipid force field. 
When I run mdrun, there is a warning saying

"Warning: 1-4 interaction at distance larger than 1
These are ignored for the rest of the simulation"

I am confused. 
What does it mean?

Cheers,

Pedro.

--
Pedro Alexandre Lapido Loureiro
Laborat?rio de F?sica Biol?gica
Instituto de Biof?sica
UFRJ
Brasil 


From jlmaccal at ucalgary.ca  Thu Aug 28 22:25:01 2003
From: jlmaccal at ucalgary.ca (Justin MacCallum)
Date: Thu Aug 28 22:25:01 2003
Subject: [gmx-users] Gromacs job locks up computer (reproducibly)
Message-ID: <1062102227.10917.23.camel@lynx.bio.ucalgary.ca>

Hi,

very interested to hear this. We have had nothing but problems with our
dual athlon 2200 MP's. They typically freeze once every week or two
while running gromacs. I'm not sure if they freeze at a reproducible
time step or not, but they are completely unresponsive and require a
reboot. We've improved the cooling, added more fans, and even moved them
to another machine room. lm_sensors reports temperatures in the low to
mid 50's (celsius) at full load. They also all use registered DDR memory
like they're supposed to. There also seems to be no pattern to which
machines are failing. They all seem to freeze at roughly random
intervals, and almost every machine (out of 16) has done it.

In short, I've been getting very frustrated with these machines, but I'm
happy to hear that there may actually be a fix. Any idea when the
environment variable check will appear? I'm going to recompile with the
suggested hacks to the cpu checks and I'll report back later.

Justin

> If it's an amd,
> 
> 1. Check if you can repeat it when compiling the standard gromacs 
> source (necessary for me to debug it, sorry :-)
> 2. cat /proc/cpuinfo and send it to me.
> 3. Try to find a file that crashes as soon as possible (30 minutes is 
> ok, 24 hours bad)
> 4. Describe it well as you can.
> 
> 
> Some background:
> 
> This is almost certainly a hardware problem in the AMD SSE 
> implementation. That is probably possible to work around, but the 
> results seem to change between different generations of the Athlon 
> CPUs, so it has been almost impossible for me to debug.
> 
> A fix (which will probably be an environment variable soon) is to edit 
> src/gmxlib/detectcpu.c and disable the SSE checking on your Athlon, 
> That way it will always use 3DNow, which is about 10% slower but rock 
> stable.
> 
> I'm sorry for the problems, but the Athlons and Pentiums are executing 
> *identical* code, and we've never seen a problem on the latter!
> 
> Cheers,
> 
> Erik

-- 
Justin MacCallum
jlmaccal at ucalgary.ca

PhD Student
Department of Biological Sciences
University of Calgary



From jlmaccal at ucalgary.ca  Thu Aug 28 22:27:01 2003
From: jlmaccal at ucalgary.ca (Justin MacCallum)
Date: Thu Aug 28 22:27:01 2003
Subject: [gmx-users] scalable PBS
Message-ID: <1062102390.10917.27.camel@lynx.bio.ucalgary.ca>

Hi,

has anyone tried scalable PBS (www.supercluster.org) yet? I'm interested
to hear anyone else's experiences with it before trying it out on our
cluster. We have a number of dual athlon boxes in our cluster which
periodically freeze. Unfortunately PBS is too stupid to handle this and
gets confused until I restart the offending nodes and then restart PBS.

Justin
-- 
Justin MacCallum
jlmaccal at ucalgary.ca

PhD Student
Department of Biological Sciences
University of Calgary



From lindahl at stanford.edu  Thu Aug 28 22:50:01 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Thu Aug 28 22:50:01 2003
Subject: [gmx-users] scalable PBS
In-Reply-To: <1062102390.10917.27.camel@lynx.bio.ucalgary.ca>
Message-ID: <D822BE3B-D998-11D7-A7AE-000A95A099E0@stanford.edu>

Hi Justin,

Scalable PBS works great (much better than pbs-2.3.16), although there 
are still some memory leaks (although the big ones were fixed). 
Freezing nodes isn't a problem (there are patches for vanilla 
PBS-2.3.16 to handle that too - look for 'scaling' patches with google).

You probably want to use it with maui-3.2.6; I'm not sure if that's 
still a prerelease, but the people at www.supercluster.org will give 
you access if you want to test it.

(Haven't tried the internal PBS scheduler with it, but my experience 
with earlier versions is that it sucks compared to maui :-)

Cheers,

Erik


On Thursday, August 28, 2003, at 01:26 PM, Justin MacCallum wrote:

> Hi,
>
> has anyone tried scalable PBS (www.supercluster.org) yet? I'm 
> interested
> to hear anyone else's experiences with it before trying it out on our
> cluster. We have a number of dual athlon boxes in our cluster which
> periodically freeze. Unfortunately PBS is too stupid to handle this and
> gets confused until I restart the offending nodes and then restart PBS.
>
> Justin
> -- 
> Justin MacCallum
> jlmaccal at ucalgary.ca
>
> PhD Student
> Department of Biological Sciences
> University of Calgary
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.



From albert_sun9 at yahoo.com  Thu Aug 28 23:08:01 2003
From: albert_sun9 at yahoo.com (Albert Sun)
Date: Thu Aug 28 23:08:01 2003
Subject: [gmx-users] ngmx:  Segmentation fault
In-Reply-To: <1061971025.5184.6.camel@werkman.bmc.uu.se>
Message-ID: <20030828210703.85654.qmail@web21502.mail.yahoo.com>

Dear David van der Spoel,
I am testing a simple case, and prepared top and gro files as attached, when I ran EM.mdp and 9atom.mdp, and see ngmx, it has the error: segmentation fault.
(em.mdp file is attached in another email)
Could you help me to have a look?
 
Thanks !      

Albert

David van der Spoel <spoel at xray.bmc.uu.se> wrote:
On Tue, 2003-08-26 at 23:32, Albert Sun wrote:
> Dear Users,
> 
> When I ran ngmx, it had error: 
> 

you give very little information. Could it be that the tpr does not
match the trajectory (in particular the tpr has not the same number of
atoms as the traj)

> " 
> 
> Reading file pul1.tpr, VERSION 3.1.2 (single precision)
> 
> trn version: GMX_trn_file
> 
> Reading frame 0 time 0.000 Opening library file
> /usr/local/gromacs/share/top/aminoacids.dat
> 
> Opening library file /usr/local/gromacs/share/top/export.dlg
> 
> Opening library file /usr/local/gromacs/share/top/bonds.dlg
> 
> Segmentation fault "
> 
> 
> Could you advise me how to solve the problem?
> 
> Thanks!
> 
> Albert
> 
> 
> 
> ______________________________________________________________________
> Do you Yahoo!?
> Yahoo! SiteBuilder - Free, easy-to-use web site design software
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.






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From albert_sun9 at yahoo.com  Thu Aug 28 23:11:01 2003
From: albert_sun9 at yahoo.com (Albert Sun)
Date: Thu Aug 28 23:11:01 2003
Subject: [gmx-users] ngmx:  Segmentation fault
In-Reply-To: <1061971025.5184.6.camel@werkman.bmc.uu.se>
Message-ID: <20030828210958.86241.qmail@web21502.mail.yahoo.com>

Dear David van der Spoel,
em.mdp and atom.ndx file are attached 
 
Thanks !      

Albert

David van der Spoel <spoel at xray.bmc.uu.se> wrote:
On Tue, 2003-08-26 at 23:32, Albert Sun wrote:
> Dear Users,
> 
> When I ran ngmx, it had error: 
> 

you give very little information. Could it be that the tpr does not
match the trajectory (in particular the tpr has not the same number of
atoms as the traj)

> " 
> 
> Reading file pul1.tpr, VERSION 3.1.2 (single precision)
> 
> trn version: GMX_trn_file
> 
> Reading frame 0 time 0.000 Opening library file
> /usr/local/gromacs/share/top/aminoacids.dat
> 
> Opening library file /usr/local/gromacs/share/top/export.dlg
> 
> Opening library file /usr/local/gromacs/share/top/bonds.dlg
> 
> Segmentation fault "
> 
> 
> Could you advise me how to solve the problem?
> 
> Thanks!
> 
> Albert
> 
> 
> 
> ______________________________________________________________________
> Do you Yahoo!?
> Yahoo! SiteBuilder - Free, easy-to-use web site design software
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.













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From nunolf at ci.uc.pt  Thu Aug 28 23:17:01 2003
From: nunolf at ci.uc.pt (Nuno R. L. Ferreira)
Date: Thu Aug 28 23:17:01 2003
Subject: [gmx-users] g_velacc again
Message-ID: <00d001c36da7$b3c4a1c0$670110ac@gandalf>

Dear all gmx users

Few days ago I asked about some hints on how to get diffusion coefficients
from VACF (Cvv(t)).

Read some stuff about the subject (Allen & Tildesley, tkx Erik) and in other
net sources.
As Anton said :

<   the integral of your VACF is exactly the same as the slope of the
positional MSD (or something similar).

If I'm not wrong,  "slope of the positional MSD" = Dt (self-diffusion
coefficient) = 1/3 * (integral of VACF) , speaking in 3D.

I've done a 100 ps MD, 2 fs of step and saving velocities every step (tkx
Anton), in a methanol box (400 molecules, tkx Christoph Freudenberger), and
tryed to compute the diffusion coefficient from MSD (g_msd) and also from
VACF (g_velacc). The Cvv(t) vs time graph shows an expected trend for this
kind of correlations (it decreases fast to some negative value, and then a
Cvv tail aproaches to zero)

g_msd gives a good value ( 2.7 +- .2 10-5 cm2 s-1), compared with the
experimental one ( 2.4 10-5 cm2 s-1).
But I "cannot manage" to obtain the value from g_velacc calculation. In
fact, I don't understand very well the output from g_velacc.
I've employed this script with the following flags:

g_velacc -f traj.trr -s traj.tpr -n

being the index file 10 methanol molecules to speed up things.
Here's the output:
COR: Correlation time (plain integral from 0.000 to 99.999 ps) = 0.01533 ps

What is this correlation time?
With -fitfn aexp , I obtain the same information as above plus:
COR: Relaxation times are computed as fit to an exponential:

COR: y = a2 exp(-x/a1)

COR: Fit to correlation function from 0.000 ps to 100.001 ps, results in a

COR: Fit from            Integral         Tail Value          Sum (ps)
a1 (ps)            a2 ()

COR: 0.0000e+00   0.0000e+00   6.0026e-02   6.0026e-02   5.1511e-02
1.1653e+00

I was expecting to get an integral value from here, but it's zero. I'm also
aware that the tail in Cvv(f) function as to be treated with special care
( Solvent diffusion outside macromolecular surfaces, Eric Lindahl & Olle
Edholm, Phys Rev. E ,V57, N1, Y1998, P791).
I used this function (aexp) cause I read somewhere (actually in a NAMD
tutorial, last summer course) that we can fit the Cvv(t) to a first order
exponential, like this :

Cvv(t) = Dt / tau * exp (-t / tau)
This example was applyed to ubiquitin in water, to calculate the Dt.

Can anibody give me some help on this? My aim is to obtain the diffusion
coefficient for a peptide. Since that for calculating MSD's of proteins with
need longer simulations, and the statisticall error with just one molecule
is "big" (MSD vs time does not show a good straight line), I was thinking in
VACF vs time. But till now I did not understood how to calculate Dt from the
information of g_velacc calculation. Where is the integral of VACF? Am I
missing something?

Many thanks,
Nuno

P.S. I apologise if my explanation is a bit confuse.














#######
Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Qu?mica Biol?gica
Departamento de Qu?mica
Faculdade de Ci?ncias e Tecnologia
Universidade de Coimbra
3004-535 Coimbra
Portugal

Phone: +351 239 852080
Fax: +351 239 827703
www.biolchem.qui.uc.pt
####




From spoel at xray.bmc.uu.se  Fri Aug 29 08:35:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Fri Aug 29 08:35:01 2003
Subject: [gmx-users] ngmx:  Segmentation fault
In-Reply-To: <20030828210703.85654.qmail@web21502.mail.yahoo.com>
References: <20030828210703.85654.qmail@web21502.mail.yahoo.com>
Message-ID: <1062139277.1739.2.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-28 at 23:07, Albert Sun wrote:
> Dear David van der Spoel,
> I am testing a simple case, and prepared top and gro files as
> attached, when I ran EM.mdp and 9atom.mdp, and see ngmx, it has the
> error: segmentation fault.
> (em.mdp file is attached in another email)
> Could you help me to have a look?

I see a system of 9 atoms in a plane which explodes after roughly 100 fs
(I decreased nstxout to 5 to see it).

If you do not see that, then I suggest you try to run it on a Linux or
Unix box first. By the way, ngmx won't work on a DOS anyway.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From spoel at xray.bmc.uu.se  Fri Aug 29 08:40:02 2003
From: spoel at xray.bmc.uu.se (David)
Date: Fri Aug 29 08:40:02 2003
Subject: [gmx-users] g_velacc again
In-Reply-To: <00d001c36da7$b3c4a1c0$670110ac@gandalf>
References: <00d001c36da7$b3c4a1c0$670110ac@gandalf>
Message-ID: <1062139544.1739.6.camel@h28n2fls34o1123.telia.com>

On Thu, 2003-08-28 at 23:02, Nuno R. L. Ferreira wrote:
> Dear all gmx users
> Can anibody give me some help on this? My aim is to obtain the diffusion
> coefficient for a peptide. Since that for calculating MSD's of proteins with
> need longer simulations, and the statisticall error with just one molecule
> is "big" (MSD vs time does not show a good straight line), I was thinking in
> VACF vs time. But till now I did not understood how to calculate Dt from the
> information of g_velacc calculation. Where is the integral of VACF? Am I
> missing something?
> 
> Many thanks,
> Nuno
> 
> P.S. I apologise if my explanation is a bit confuse.
> 
> 
Have you looked at the graph in xmgrace? It is probably easiest to start
there, use the integration function to see how ill-behaved the ACF is.
It may just fluctuate wildly. Then use the non-linear fit to fit your
ACF to a function of your choosing and integrate again. You can probably
get the same result from gromacs if you use some more flags like
-beginfit and -endfit

> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> #######
> Nuno Ricardo Santos Loureiro da Silva Ferreira
> Grupo de Qu?mica Biol?gica
> Departamento de Qu?mica
> Faculdade de Ci?ncias e Tecnologia
> Universidade de Coimbra
> 3004-535 Coimbra
> Portugal
> 
> Phone: +351 239 852080
> Fax: +351 239 827703
> www.biolchem.qui.uc.pt
> ####
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From albert_sun9 at yahoo.com  Fri Aug 29 15:59:01 2003
From: albert_sun9 at yahoo.com (Albert Sun)
Date: Fri Aug 29 15:59:01 2003
Subject: [gmx-users] ngmx:  Segmentation fault
In-Reply-To: <1062139277.1739.2.camel@h28n2fls34o1123.telia.com>
Message-ID: <20030829135827.73411.qmail@web21505.mail.yahoo.com>

thanks -  David!

David <spoel at xray.bmc.uu.se> wrote:On Thu, 2003-08-28 at 23:07, Albert Sun wrote:
> Dear David van der Spoel,
> I am testing a simple case, and prepared top and gro files as
> attached, when I ran EM.mdp and 9atom.mdp, and see ngmx, it has the
> error: segmentation fault.
> (em.mdp file is attached in another email)
> Could you help me to have a look?

I see a system of 9 atoms in a plane which explodes after roughly 100 fs
(I decreased nstxout to 5 to see it).

If you do not see that, then I suggest you try to run it on a Linux or
Unix box first. By the way, ngmx won't work on a DOS anyway.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.


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From albert_sun9 at yahoo.com  Fri Aug 29 18:19:01 2003
From: albert_sun9 at yahoo.com (Albert Sun)
Date: Fri Aug 29 18:19:01 2003
Subject: [gmx-users] ngmx:  Segmentation fault
In-Reply-To: <20030829135827.73411.qmail@web21505.mail.yahoo.com>
Message-ID: <20030829161752.50615.qmail@web21507.mail.yahoo.com>

Hi, David, 
Do you know what is the reason that atoms explod? 
Is it because that I did not include bond force and constraints or other wrong parameters?
 
thanks!
 
 
 
   

David <spoel at xray.bmc.uu.se> wrote: On Thu, 2003-08-28 at 23:07, Albert Sun wrote:
> Dear David van der Spoel,
> I am testing a simple case, and prepared top and gro files as
> attached, when I ran EM.mdp and 9atom.mdp, and see ngmx, it has the
> error: segmentation fault.
> (em.mdp file is attached in another email)
> Could you help me to have a look?

I see a system of 9 atoms in a plane which explodes after roughly 100 fs
(I decreased nstxout to 5 to see it).

If you do not see that, then I suggest you try to run it on a Linux or
Unix box first. By the way, ngmx won't work on a DOS anyway.


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.


---------------------------------
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Yahoo! SiteBuilder - Free, easy-to-use web site design software


---------------------------------
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From spoel at xray.bmc.uu.se  Fri Aug 29 18:46:01 2003
From: spoel at xray.bmc.uu.se (David)
Date: Fri Aug 29 18:46:01 2003
Subject: [gmx-users] ngmx:  Segmentation fault
In-Reply-To: <20030829161752.50615.qmail@web21507.mail.yahoo.com>
References: <20030829161752.50615.qmail@web21507.mail.yahoo.com>
Message-ID: <1062175907.1735.6.camel@h28n2fls34o1123.telia.com>

On Fri, 2003-08-29 at 18:17, Albert Sun wrote:
> Hi, David, 
> Do you know what is the reason that atoms explod? 
> Is it because that I did not include bond force and constraints or
> other wrong parameters?
Anything, charged atoms with no van der waals or something like that.
Something in your topology. If you give all atoms zero charge and a
reasonable vanderwaals params it will work fine.
>  
> thanks!
>  
>  
>  
>    
>         David <spoel at xray.bmc.uu.se> wrote: 
>                 On Thu, 2003-08-28 at 23:07, Albert Sun wrote:
>                 > Dear David van der Spoel,
>                 > I am testing a simple case, and prepared top and gro
>                 files as
>                 > attached, when I ran EM.mdp and 9atom.mdp, and see
>                 ngmx, it has the
>                 > error: segmentation fault.
>                 > (em.mdp file is attached in another email)
>                 > Could you help me to have a look?
>                 
>                 I see a system of 9 atoms in a plane which explodes
>                 after roughly 100 fs
>                 (I decreased nstxout to 5 to see it).
>                 
>                 If you do not see that, then I suggest you try to run
>                 it on a Linux or
>                 Unix box first. By the way, ngmx won't work on a DOS
>                 anyway.
>                 
>                 
>                 -- 
>                 Groeten, David.
>                 ________________________________________________________________________
>                 Dr. David van der Spoel, Dept. of Cell and Molecular
>                 Biology
>                 Husargatan 3, Box 596, 75124 Uppsala, Sweden
>                 phone: 46 18 471 4205 fax: 46 18 511 755
>                 spoel at xray.bmc.uu.se spoel at gromacs.org
>                 http://xray.bmc.uu.se/~spoel
>                 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>                 _______________________________________________
>                 gmx-users mailing list
>                 gmx-users at gromacs.org
>                 http://www.gromacs.org/mailman/listinfo/gmx-users
>                 Please don't post (un)subscribe requests to the list.
>                 Use the 
>                 www interface or send it to
>                 gmx-users-request at gromacs.org.
>         
>         
>         ______________________________________________________________
>         Do you Yahoo!?
>         Yahoo! SiteBuilder - Free, easy-to-use web site design
>         software
> 
> 
> ______________________________________________________________________
> Do you Yahoo!?
> Yahoo! SiteBuilder - Free, easy-to-use web site design software
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


From nunolf at ci.uc.pt  Fri Aug 29 19:27:01 2003
From: nunolf at ci.uc.pt (Nuno R. L. Ferreira)
Date: Fri Aug 29 19:27:01 2003
Subject: [gmx-users] g_velacc again
References: <20030829100002.27516.75015.Mailman@hawk.theophys.kth.se>
Message-ID: <012901c36e52$ee3b1950$670110ac@gandalf>

David wrote:
> Have you looked at the graph in xmgrace? It is probably easiest to start
> there, use the integration function to see how ill-behaved the ACF is.
> It may just fluctuate wildly. Then use the non-linear fit to fit your
> ACF to a function of your choosing and integrate again. You can probably
> get the same result from gromacs if you use some more flags like
> -beginfit and -endfit

I've done the integration and the value is similar to the correlation time
given by g_velacc. So basically the Correlation time is the VACF integral?
But if it is, why does it come in ps? Should't be in nm2.s-1 or something
similar ?

Also, I've done the calculation with -normalize. After new try
with -nonormalize the value that comes out is:
COR: Correlation time (plain integral from 0.000 to 99.999 ps) = 0.986 ps
(by integration of Cvv(t) vs time graph, the value is similar (0.980).
Applying the formula given in last e-mail, and considering that velocities
come in nm.s-1 , I get a value of
Dt = 3.2 10-5 m2.s-1 (Dt exp. = 2.4 10-9 cm2.s-1).
So, I think that some units are wrong (a factor of 10-4).

Regards,
Nuno




From s8026264 at sepahan.iut.ac.ir  Sun Aug 31 16:57:01 2003
From: s8026264 at sepahan.iut.ac.ir (s8026264)
Date: Sun Aug 31 16:57:01 2003
Subject: [gmx-users] Steepest descent and max(|F|)
Message-ID: <20030831112100.M37527@sepahan.iut.ac.ir>

Dear All

In the manual you use max(|Fn|),Why don't you use |Fn| ?

The notation max(|Fn|) means the largest of the absolute values of the force
components.

The notation |Fn| means the absolute values of the force.


Good Luck

Mojtaba Alaei  




From lindahl at stanford.edu  Sun Aug 31 17:29:00 2003
From: lindahl at stanford.edu (Erik Lindahl)
Date: Sun Aug 31 17:29:00 2003
Subject: [gmx-users] Steepest descent and max(|F|)
In-Reply-To: <20030831112100.M37527@sepahan.iut.ac.ir>
Message-ID: <8090ECEE-DBC7-11D7-8F96-000A95A099E0@stanford.edu>

Hi,

It's a bit hard to tell without knowing what page in the manual you are 
referring to, but considering there is an index 'n' my bet would be 
that it means the maximum force on any single atom in the system.

Cheers,

Erik

On Sunday, August 31, 2003, at 04:34 AM, s8026264 wrote:

> Dear All
>
> In the manual you use max(|Fn|),Why don't you use |Fn| ?
>
> The notation max(|Fn|) means the largest of the absolute values of the 
> force
> components.
>
> The notation |Fn| means the absolute values of the force.
>
>
> Good Luck
>
> Mojtaba Alaei
>
>
> _______________________________________________
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