[gmx-users] Re: GPCR MD Tutorial Using GROMACS (URL)

Anirban Ghosh reach.anirban.ghosh at gmail.com
Fri Apr 27 11:38:30 CEST 2012

On Fri, Apr 27, 2012 at 1:01 PM, Bala S <think_beyond at aol.com> wrote:

> Dear Justin
> Thanks for the explanation.
> I am following your tutorial of KALP membrane simulation. I am stuck in
> between two steps of InflateGRO. After the first step, the tutorial
> requests
> to perform EM. Should I be running grompp with new system_inflated.gro file
> to generate a new .tpr file for EM or should I perform EM with em.tpr
> which

was generated some time back in the tutorial?

You should run grompp with the inflated .gro file (system_inflated.gro)
since you will be minimizing the inflated .gro file after every compression
step to remove bad contacts. The earlier em.tpr was used to remove
periodicity of the bilayer only.

> The latter ran EM but the
> former shows error 'number of coordinates in coordinate file
> (system_inflated.gro, 6438)
>             does not match topology (topol.top, 17403)"

The difference in atom numbers might be because your .top file contains
some extra molecules in the [ molecules ] section (may be SOL). Use .top
file that contains only protein and lipid molecules.

> Thanks.
> Bala S
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