[gmx-users] Re: gmx-users Digest, Vol 3, Issue 63

Wed Jul 28 07:42:35 CEST 2004

----------------------
Mohd Anwaruddin, M.Sc.
C/o DR.H.A.Nagarajaram,
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD),
Nacharam,
Hyderabad-500 076, INDIA.
Tel : +91-40-27151344 ext 1207,1208.
anwar_m1 at rediffmail.com
-----------------------

---------REPLY TO-------------
Date:Tue Jul 27 16:16:15 CST 2004
FROM: gmx-users-request at gromacs.org
To: gmx-users at gromacs.org
Subject: gmx-users Digest, Vol 3, Issue 63
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Today's Topics:

   1. Re: error (Bert de Groot)
   2. Re: atoms (Anton Feenstra)
   3. Re: problem in protein - cofactor linkage (Anton Feenstra)
   4. Re: The meaning of rlist, rvdm and rcolumn (Anton Feenstra)
   5. RE: The meaning of rlist, rvdm and rcolumn (Li Dawei)
   6. Re: SUSPICIOUS: Pressure scaling ... (Anton Feenstra)
   7. Re: how to calculate water residence time? (Anton Feenstra)
   8. Re: Constraint algorithm error (Anton Feenstra)
   9. Re: Problem with CG in double precision (Anton Feenstra)

---------------------------------------------------------------------- 

Message: 1
Date: Tue, 27 Jul 2004 09:01:40 +0200
From: Bert de Groot <bgroot at gwdg.de>
Subject: Re: [gmx-users] error
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4105FDD4.1060007 at gwdg.de>
Content-Type: text/plain; charset=us-ascii; format=flowed

Dinesh Pinisetty wrote:
> 
> 
> 
> Hello all,
>      This is my second question please someone reply me about the
> information on atom types.
> Could anyone explain me what this error mean:
> FATAL ERROR: Found a second defaults directive, file "lipid.itp", line 
9. 
> Please explain me this what this error mean what should be done to avoid 
> this error.

Hi Dinesh,

If you use the following set of parameters:
http://www.gromacs.org/topologies/uploaded_force_fields/ffgmx_lipids.tar.gz 

then you don't need lipid.itp anymore (the lipid parameters are integrated 
in the ff*itp files) 
and hence you get rid of the error.

--

Bert

____________________________________________________________________________ 
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________ 

------------------------------

Message: 2
Date: Mon, 26 Jul 2004 17:41:41 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] atoms
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <41052635.7060300 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed

Dinesh Pinisetty wrote:
> 
> 
> 
> Hi all,
> Could anyone please tell me where I can get the full forms of all the 
> atomtypes used in pdb files and .itp files.If suppose I want to know 
the 
> full form of atomtypes 'LO' or 'LOM' or 'CA' etc which are present in 
the 
> lipid.itp files of Dr.Tielmans website,where should I refer to.

What do you mean by 'full form'? The [atomtypes] section defines the mass, 
LJ parameters and charge. What else is there to know?

-- 
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) | 
|_____________|_______________________________________________________| 

------------------------------

Message: 3
Date: Tue, 27 Jul 2004 09:51:10 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] problem in protein - cofactor linkage
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4106096E.8050708 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed

pankaj at cdfd.org.in wrote:

> Dear All,
> 
> I am simulating a protein having PLP co-factor. PLP has a covalent linkage 
> with a lysine residue of the protein.
> 
> I got the topology for the PLP from PRODRG server and included it as 
itp 
> file. But the covalent bond has not been formed. In the simulation the 
> cofactor moves away from the protein probably due to the non-existance 
> of the covalent bond interaction.
> 
> Later I included a line in the specbond.dat file specifying the PLP-LYS 
> linkage and copied it into the working directory and ran the simulation. 
> Even this time the PLP has moved away from the protein, which means that 
> the covalent bond is not still formed.
> 
> I feel that the specbond.dat entry will be read only when the residue 
type 
> of PLP is defined in the rtp file. Is this correct ?
> How can the covalent bond between the protein and PLP be made ?

That is right - pdb2gmx parses the specbonds while it builds your molecule 
from rtp buildingblocks.

There are ways you could solve this:
1) convert the .itp file for PLP to an rtp entry. That isn't much work, 
it 
is mainly a matter of changing atom numbers into atom names and possibly 
rearranging some columns. There is a set of scripts 'Gromacs Topology tools' 
in the contributions section, nr2nametop is the one you could use. 
2) Manually 'add' your PLP topology to the protein topology. Again you 
can 
use my top tools. First run nr2nametop on your PLP. Then add each of the 
[atoms], [bonds], [angles] section from PLP to the end of the correpsonding 
section of your protein. THen manually add the bond from PLP to protein, 
and finally run renumtop to change all atom labels back to atom numbers. 

If your have problems using the scripts, ask me again. They generatlly 
work 
like:
# renumtop < merged.top > renumbered.top

(Come to think of it, it would not be difficult to make a script that merges 
two (or more) topologies automatically...)

-- 
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) | 
|_____________|_______________________________________________________| 

------------------------------

Message: 4
Date: Tue, 27 Jul 2004 10:00:20 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] The meaning of rlist, rvdm and rcolumn
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <41060B94.9060205 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed

Li Dawei wrote:

> Dear all:
> 
> I searched this mailing list but become even more confused. Who can help 
> to clarify the exact meaning of these parameters. 

[...]

> http://www.gromacs.org/pipermail/gmx-users/2002-June/028443.html
> http://www.gromacs.org/pipermail/gmx-users/2003-January/030507.html

these links are dead...

[...]

> this implies: rlist > rvdw,rcoulomb > r*_switch
> ... in contrast to (part of) the docu, and the
> errormsg given by the code, and to one of the
> messages cited above.(the message of Anton
> Feenstra reminds me rather of another concept,
> namely the multiple timestep algoritm which, if 
> I am not mistaken, is not implemented
> in Gromacs)

Your explanation seems correct to me. rlist is the cutoff
for neighbour searching, i.e. each nstlist steps all atoms
within rlist are put in the neighborlists and forces are
evaluated. Each step, all atom pairs in the neighborlists
are checked against rvdw and rcoul and forces are evaluated
for all distances below these cutoffs.

-- 
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) | 
|_____________|_______________________________________________________| 

------------------------------

Message: 5
Date: Tue, 27 Jul 2004 16:05:06 +0800
From: "Li Dawei" <phyldw at nus.edu.sg>
Subject: RE: [gmx-users] The meaning of rlist, rvdm and rcolumn
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
	<BE1BD75EBBF5694E96A4FD443826AA7E019597B0 at MBXSRV06.stf.nus.edu.sg>
Content-Type: text/plain;	charset="us-ascii"

Dear Anton:

Thanks for your reply. But why grompp requir that rlist<=rvdm? It is
terrible.

This is in the menu of 3.2
********************************************************************
vdwtype:
Cut-off 
Twin range cut-off's with neighbor list cut-off rlist and VdW cut-off
rvdw, where rvdw >= rlist. 
************************************************************************ 
**

Li, Dawei

------------------------------

Message: 6
Date: Tue, 27 Jul 2004 10:07:22 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] SUSPICIOUS: Pressure scaling ...
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <41060D3A.2040607 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed

Tandia, Adama wrote:

> Dear ALL:
> I'm running (or trying to run) a MD with the following .mdp file ( s 
system composed of 10 different ions) 
> A room temperature and 1 bar:
[...]
> I searched the user list and I tried many different values of tau_p (from 
0.1 to 70 (!) )but that did not help at all. 
> The same .mdp file adapted to Si only works perfectly!

You do not explain what your problem is. Which error mesage(s) do you get? 

Is there a reason to couple each type of ion to a separate temperature 
bath? In general, if they are sufficiently in contact with each other, 
energy exchange should be sufficient to equilibrate temperature differences, 
and you could (and should) couple the whole system to one bath.

Two baths are generally used for a large solute in solvent (e.g. protein 
in water) where energy echange at the solute-solvent interface may be
limited.

-- 
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) | 
|_____________|_______________________________________________________| 

------------------------------

Message: 7
Date: Mon, 26 Jul 2004 17:48:35 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] how to calculate water residence time?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <410527D3.6030302 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed

Linda wrote:

> Hi, all,
> 
> Does gromacs analysis tool can calculate the water residence time around 
a group like negative charged group or hydrophobic group? If so, which 
one? 

g_hbond can at least calculate hydrogen bonds formed. I don't know if it 
can do autocorrelations to estimate residence time, but you may be able 
to do that yourself (e.g., using xmgrace).

-- 
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) | 
|_____________|_______________________________________________________| 

------------------------------

Message: 8
Date: Mon, 26 Jul 2004 17:55:37 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] Constraint algorithm error
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <41052979.2080307 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed

nicolas Dinter wrote:

> Anton,
> 
> Seeing that it was a constraint error I ran a NPT simulation, without 
any 
> constraint (mdp-itp),
> then my calcul runs for about 9.845ps (for a 10ps sim) and crash for 
> pressure scaling error (tau_p=10 ps, ref_p=1bar), and thus with a very 
small 
> time step (0.00001 ps)to avoid this error. But more surprizing the box 
size 
> do not change at all! Being far from the equilibrium density I am surprized. 

That is to be expected with tau_p = 10 ps if you only run for 10 ps!

-- 
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) | 
|_____________|_______________________________________________________| 

------------------------------

Message: 9
Date: Mon, 26 Jul 2004 17:45:49 +0200
From: Anton Feenstra <feenstra at chem.vu.nl>
Subject: Re: [gmx-users] Problem with CG in double precision
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4105272D.3040708 at chem.vu.nl>
Content-Type: text/plain; charset=us-ascii; format=flowed

anwar at cdfd.org.in wrote:

> Dear users,
> I am getting a problem with CG minimization of protein in Double Precision. 
> The error is 
...
> I kept none constrains in em.mdp.

Do you use dummy atom constructions as generated by 'pdb2gmx -dummy'?

I have not used dummy in 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) | 
|_____________|_______________________________________________________| 

------------------------------

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End of gmx-users Digest, Vol 3, Issue 63
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