[gmx-users] Settle and Virial
Rahul Godawat
godawr at rpi.edu
Fri May 5 09:28:31 CEST 2006
Hi All,
I am wondering how can I get contributions from Settle ( is there any ?)
algorithm to the virial or pressure tensor calculations for simulation of
pure water. I assume there should not be any.
Thanks
Rahul
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Today's Topics:
1. Re: REMD in one nodes with two processors (Dongsheng Zhang)
2. RE: Problems with pdb2gmx and grompp (Dallas B. Warren)
3. install problem (James Rustad)
4. Re: Problems with pdb2gmx and grompp (Yang Ye)
5. Intra x inter coulombic and van-der-waals terms (Jones de Andrade)
6. g_hbond range checking error (Dallas B. Warren)
----------------------------------------------------------------------
Message: 1
Date: Thu, 04 May 2006 16:59:16 -0400
From: Dongsheng Zhang <dong at pampas.chem.purdue.edu>
Subject: Re: [gmx-users] REMD in one nodes with two processors
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1146776356.6129.9.camel at pampas.chem.purdue.edu>
Content-Type: text/plain
David,
Thank you. My mdrun_mpi has problems with parallel computing. I don't
know why. I recompile gromacs, then it works now. I have saved the old
Makefile before "make distclean". I find it is the same as the new
Makefile, then I don't understand why the old mdrun_mpi didn't work.
Thank you very much for your help!
Dongsheng
On Thu, 2006-05-04 at 21:52 +0200, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > Thank you, David. I try it as:
> >
> >
> > mpirun -np 2 n1 /home/brasilia/dong/mdrun_mpi -replex 500 -reseed
> > -1 -s replica -v >& zevel
> >
> > It gives me the same error message: Can not open file: replica.tpr
> >
> was mdrun compiled with MPI? are you sure the second copy of mdrun is in
> the right directory? try it from your home directory
>
> > Any other suggestions?
> >
> > Thanks!
> >
> >
> > Dongsheng
> >
> >
> > On Thu, 2006-05-04 at 20:17 +0200, David van der Spoel wrote:
> >> Dongsheng Zhang wrote:
> >>> Dear David,
> >>>
> >>> I had tried mpirun before, it didn't work either. the command was:
> >>> mpirun -np 2 n1 /home/brasilia/dong/mdrun_mpi_MC -replex 500 -reseed
-1
> >>> -multi -s replica -deffnm replica -N 2 -v >& zevel
> >> remove the -N 2 -multi -deffnm replica options and try again.
> >>
> >>
> >>> Because the two processors are in one node, so I changed my command
to
> >>> ( and go to the local node n1 to submit the job):
> >>>
> >>> /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi -s
> >>> replica -deffnm replica -N 2 -v >& zevel
> >>>
> >>> Could you please tell me if there is any way to check if the program
can
> >>> recognize -multi option?
> >>>
> >>> Thank you!
> >>>
> >>>
> >>> Dongsheng
> >>>
> >>>
> >>>
> >>> On Thu, 2006-05-04 at 19:13 +0200, David van der Spoel wrote:
> >>>> Dongsheng Zhang wrote:
> >>>>> Marcus,
> >>>>>
> >>>>> Thank you for your suggestion. I try it. The computer gives me the
same
> >>>>> error message. The problem is that the program always looks for
> >>>>> replica.tpr instead of replica0.tpr and replica1.tpr. I don't know
why.
> >>>>>
> >>>> use mpirun
> >>>> search mailinglist
> >>>>> Best wishes!
> >>>>>
> >>>>>
> >>>>> Dongsheng
> >>>>>
> >>>>>
> >>>>> On Thu, 2006-05-04 at 18:38 +0200, Marcus Kubitzki wrote:
> >>>>>> If you use the -deffnm option, you do not need -s, b/c it is
> >>>>>> already accounted for with the -deffnm.
> >>>>>> Marcus
> >>>>>>
> >>>>>> Dongsheng Zhang wrote:
> >>>>>>> David,
> >>>>>>>
> >>>>>>> Thank you for your reply. I have provided replica0.tpr and
replica1.tpr,
> >>>>>>> but the program looks for replica.tpr. It surprises me.
> >>>>>>>
> >>>>>>> I have also tried to run
> >>>>>>>
> >>>>>>> /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1 -multi
-s
> >>>>>>> replica0 replica1 -deffnm replica -N 2 -v >& zevel
> >>>>>>> It doesn't work either (complains only one replica: Nothing to
exchange
> >>>>>>> with only one replica). it seems the program does not recognize
the
> >>>>>>> -multi option.
> >>>>>>>
> >>>>>>>
> >>>>>>> Best wishes!
> >>>>>>>
> >>>>>>>
> >>>>>>> Dongsheng
> >>>>>>>
> >>>>>>>
> >>>>>>> On Thu, 2006-05-04 at 18:11 +0200, David van der Spoel wrote:
> >>>>>>>
> >>>>>>>> Dongsheng Zhang wrote:
> >>>>>>>>
> >>>>>>>>> Dear gmx users,
> >>>>>>>>>
> >>>>>>>>> I have trouble to run REMD on one node with two processors. The
command
> >>>>>>>>> I used is
> >>>>>>>>> /home/brasilia/dong/mdrun_mpi -np 2 -replex 500 -reseed -1
-multi -s
> >>>>>>>>> replica -deffnm replica -N 2 -v >& zevel
> >>>>>>>>>
> >>>>>>>>> the error message is:
> >>>>>>>>>
> >>>>>>>>> Can not open file:
> >>>>>>>>> replica.tpr
> >>>>>>>> you need replica0 and replica1.tpr
> >>>>>>>>
> >>>>>>>>> This error message looks strange to me. Because I have used
-multi, the
> >>>>>>>>> program should look for replica0.tpr and replica1.tpr. Could
anyone
> >>>>>>>>> point out what's wrong in my command?
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Thank you in advance!
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> Dongsheng
> >>>>>>>>> _______________________________________________
> >>>>>>>>> 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
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> >>>>>>> _______________________________________________
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------------------------------
Message: 2
Date: Fri, 05 May 2006 10:26:44 +1000
From: "Dallas B. Warren" <Dallas.Warren at vcp.monash.edu.au>
Subject: RE: [gmx-users] Problems with pdb2gmx and grompp
To: edumlopes at yahoo.com.br, Discussion list for GROMACS users
<gmx-users at gromacs.org>
Message-ID:
<89907EA1DCFB7548A431C13A270F9DD5019F3091 at prk-exch-01.vcp.local>
Content-Type: text/plain; charset=us-ascii
>Always having the very same problem using pdb2gmx (in order to generate
the .ndx, .gro and .top files),
>it complained about not finding neither DPP nor DPPC in the residues
library. To solve this problem I
The problem is that the residue is not in the residue library, as the
error states. And the residue library is stored in the rtp file.
You only use pdb2gmx when you have a protein like molecule with residues
linked together in some chain which you need to generate the topology
for, and they have to have entries in the database. Typically the .rtp
file only contains residues for building proteins. When you are working
with lipids, as you are here, you don't use that script since you
already have all the .itp, .top, .gro files etc required to run the
simulation. Simply skip that step all together.
Catch ya,
Dr. Dallas Warren
Lecturer
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 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
------------------------------
Message: 3
Date: Thu, 4 May 2006 18:21:03 -0700
From: "James Rustad" <james.rustad at gmail.com>
Subject: [gmx-users] install problem
To: gmx-users at gromacs.org
Message-ID:
<e49ca7a20605041821y1c5615besa3f91ae48caa8e04 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear GMX List,
I am running into an installation problem with a recent version of the
pathscale compiler
when trying
./configure --enable-mpi
I get
"checking size of int... configure: error: cannot compute sizeof (int), 77"
I searched the list and saw a similar problem with xlc, but no solution..
Is there a workaround for this?
Jim Rustad
------------------------------
Message: 4
Date: Fri, 05 May 2006 10:00:23 +0800
From: Yang Ye <leafyoung81-group at yahoo.com>
Subject: Re: [gmx-users] Problems with pdb2gmx and grompp
To: edumlopes at yahoo.com.br, Discussion list for GROMACS users
<gmx-users at gromacs.org>
Message-ID: <445AB1B7.3040308 at yahoo.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
you shall have sections of
[ system ]
[ molecules ]
A 1
B ...
in the end of your top
Yang Ye
Eduardo Martins Lopes wrote:
> Greetings fellows, after i successfully installed the gromacs I had
> some success simulating simple systems but when it comes to a DPPC
> bilayer, i got the "old" DPP or DPPC residue not found in library.
>
> I did a deep research at the users list but none of the sugestions
> worked for me.
>
> To start playing around with Gromacs, I got the Prof. Tielman's
> DPPC.pdb, lipid.itp, dppc.itp, example2.top . I also got the benchmark
> files to try it out. Also got the modified ffG43a2x and every other
> modified force fields files I could find.
>
> Always having the very same problem using pdb2gmx (in order
> to generate the .ndx, .gro and .top files), it complained about not
> finding neither DPP nor DPPC in the residues library. To solve this
> problem I tried many things like:
>
> 1- I hacked the ffG43a2.itp inserting #include lipid.itp and dppc.itp
> but no improvements achieved
> 2 - Insert the lipid.itp data into ffG43a2.rtp file. The
> message changed to problem with .rtp file at line (nothing else)
> 3 - Removed the bad data of the .rtp file and then I modified the .hdb
> file but the message changed back to DPP (DPPC) residue not found in
> library
> 4 - I renamed the entire set of ffG43a2x files to ffG43a2 (backing up
> the old files) but the error messaged came back to the rtp. file problem.
>
> I found many many replies for this very same problem, but as I said,
> none of them could help me.
>
> After giving up on pdb2gmx, I went back to the benchmark files and
> tried to work with it (as I read on one of the list messages). I just
> modified the .top (DPPC 1) to fit my system. As you may noticed, i
> simplified my old system to 1 molecule.
>
> I had the same problem on pdb2gmx. But i went forward and tried
> to generate the .tpr file using grompp. This is the error:
> "Fatal error:
> number of coordinates in coordinate file
> (/home/debora/dppc/1dppcH.gro, 50)
> does not match topology (/home/debora/dppc/1dppcH.top, 0)"
>
> I went to http://davapc1.bioch.dundee.ac.uk/prodrg/ and inserted my
> pdb file there...I used the .gro, .top and the .pdb file (with H's)
> there and tried to generate the .tpr file...I got the sabe "not
> matching" error
> "Fatal error:
> number of coordinates in coordinate file
> (/home/debora/dppc/1dppcH.gro, 50)
> does not match topology (/home/debora/dppc/1dppcH.top, 0)"
>
> I really appreciate any hint on what should I do.
>
> Thanks in advance.
>
> Eduardo Martins Lopes
> Undergratuate Student at Universidade Federal de São Carlos UFSCar -
> SP Brazil
>
>
> ------------------------------------------------------------------------
> Abra sua conta no Yahoo! Mail
>
<http://us.rd.yahoo.com/mail/br/tagline/mail/*http://br.info.mail.yahoo.com/
>
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------------------------------
Message: 5
Date: Thu, 4 May 2006 23:54:54 -0300
From: "Jones de Andrade" <johannesrs at gmail.com>
Subject: [gmx-users] Intra x inter coulombic and van-der-waals terms
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<54e4355e0605041954w50e9188di5c4a3aff0851aefd at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi!
Sorry if this message reaches the list twice, but Gmail doesn't let me know
if the list received it... seems that it stores somehow in the same message
if it comes back, so I just know when there are answers. :(
Anyway, thanks a lot in advance for any help in this subject!
Yours,
Jones
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
Hi!
Well, I was trying to calculate the intermolecular total energy of
some long systems here, when I got locked in a problem.
g_energy allows me to isolate Coulomb-(SR), Coulomb-14 and
Coul.-recip. for the coulombic terms, for example. The seems to be
that, in long chain molecules (by long, I mean more than 1-4 maximum
distance), the program outputs the 1-n (n>4) intramolecular terms of
the interactions together with most of the other intermolecular
coulombic terms in Coulomb-(SR) (exception for the molecules so far
that are in the Coul.-recip. part, but my molecules are some times
smaller than any cutoff radius used).
I would like to know if there is any work-around for this, in order to
remove the 1-n (n>4) intramolecular terms from the other
intermolecular total energies I get.
Just in time: I tried to increase, in the topology file, the nrexcl
(to 9, the largest number of bonds between two atoms in the molecules
simulated) parameter. It helped a lot, and started to yeld really
better values. But, on the other hand, it also yelded very different
trajectories, probably due to changes in conformation as a consequence
of the lack of forces derived from those intramolecular interactions
it excluded. :(
Does anybody have any idea of how to deviate from this problem?
Thanks a lot in advance!
Jones
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Message: 6
Date: Fri, 05 May 2006 13:20:50 +1000
From: "Dallas B. Warren" <Dallas.Warren at vcp.monash.edu.au>
Subject: [gmx-users] g_hbond range checking error
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
<89907EA1DCFB7548A431C13A270F9DD5019F315C at prk-exch-01.vcp.local>
Content-Type: text/plain; charset=us-ascii
Using this command:
############################
g_hbond -f ../76.55-78.95ns.xtc -s ../md_000.tpr -n index.ndx -num
hbnum_MGL-MGL
############################
I get this output:
############################
Reading file ../md_000.tpr, VERSION 3.2 (single precision)
Note: tpx file_version 31, software version 40
Specify 2 groups to analyze:
Group 0 ( DGL) has 158400 elements
Group 1 ( MGL) has 100800 elements
Group 2 ( DGL_MGL) has 259200 elements
Select a group: 1
Selected 1: 'MGL'
Select a group: 1
Selected 1: 'MGL'
Calculating hydrogen bonds in MGL (100800 atoms)
Found 9600 donors and 19200 acceptors
Reading frame 0 time 76550.000
Will do grid-seach on 44x46x52 grid, rcut=0.35
-------------------------------------------------------
Program g_hbond, VERSION 3.3
Source code file: gmx_hbond.c, line: 665
Range checking error:
Variable gx has value -24. It should have been within [ 0 .. 44 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
############################
Just doing what it tells me to ;-)
When I get the chance I will upgrade to 3.3.1, but couple of things
running that I have to leave for the moment.
Catch ya,
Dr. Dallas Warren
Lecturer
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 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
------------------------------
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