[gmx-users] Model of water

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Oct 6 16:45:07 CEST 2012

Yes, the system is only POPC and water. 


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
Sent: Saturday, October 6, 2012 6:07 PM
Subject: Re: [gmx-users] Model of water

On 10/6/12 10:32 AM, Shima Arasteh wrote:
> OK.
> I did as follow as I described, but there is an error:
> 1.editconf -f popc.pdb -o popc-newbox.gro -c -d 1.0 -bt cubic
> 2.genbox -cp popc-newbox.gro -cs spc216.gro -o popc-solv.gro -p topol.top
> Then added #include "charmm36.ff/tip3p.itp" to topol.top
> 3.grompp -f em.mdp -c popc-solv.gro -p topol.top -o em.tpr
> Fatal error:
> number of coordinates in coordinate file (popc-solv.gro, 74672)
>               does not match topology (topol.top, 104936)
> I checked the water molecules of popc-solv.gro by grep command ;
> # grep -c HW popc-solv.gro
> 48696
> [ molecules ]
> ; Compound        #mols
> POPC              238
> SOL             24348
> What is the problem? would you please help me? I think the SOL molecule are counted twice!!

You're off by a huge amount of atoms, so something is very wrong.  The water 
molecules do not appear to be the problem.  The number of HW/2 is equal to the 
number of SOL molecules.  Is the system only POPC in water?  No protein or any 
other components?



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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