[gmx-users] protein membrane system

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Dec 25 18:53:04 CET 2012

In order to compare the first and the second .gro file, I used grep -c OW (file.gro) to see how many waters exist in my new system. I got 22352, however I got 23703 before ( when I had not deleted the disturbing water molecules). So 23703-22352=1351 molecules.
Also I compared the atom noumbers in two .gro files( .gro files : before and after deleteing disturbing water molecules):
Before: 103723
After: 99625
Then 103723-99652=4071 divided by 3 gets: 1357 molecules.
There is a difference between 2 answer. 6 molecules! What's wrong? I am sure that I have just deleted water molecules by VMD.
Any body helps me  please?

I would appreciate you.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, December 25, 2012 4:56 PM
Subject: Re: [gmx-users] protein membrane system

On 12/25/12 2:42 AM, Shima Arasteh wrote:
> Hi all,
> I'm trying to simulate a system of POPC- Protein- Water- Ion following the Justin's tutorial of Kalp15-DPPC.
> I get the system-solved-ion.gro and run energy minimization. I saw some water molecules in em.gro file, therefore, I erase them and then again save the .gro file as a new one.
> But when I make a new index file, updated the top file and then go through the NVT simulation, I get this fatal error:
> Warning: atom name 33908 in topol.top and em.gro does not match (HW2 - HW1)
> Warning: atom name 33909 in topol.top and em.gro does not match (OW - HW2)
> Warning: atom name 33910 in topol.top and em.gro does not match (HW1 - OW)
> (more than 20 non-matching atom names)
> WARNING 1 [file topol.top, line 57]:
>    43770 non-matching atom names
>    atom names from topol.top will be used
>    atom names from em.gro will be ignored
> Setting gen_seed to 2957
> Velocities were taken from a Maxwell distribution at 310 K
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/readir.c, line: 1406
> Fatal error:
> 38 atoms are not part of any of the T-Coupling groups
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------

The mismatch implies that your atom mapping is off by one entry, indicating that 
either the update to your topology is wrong or that you deleted only part of 
some molecule, leaving a fractional species somewhere.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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