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

[Anirban Ghosh]

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
>
>
> --
> View this message in context:
> http://gromacs.5086.n6.nabble.com/GPCR-MD-Tutorial-Using-GROMACS-URL-tp4930034p4933137.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120427/99ec4539/attachment.html>