On Fri, Apr 27, 2012 at 1:01 PM, Bala S <think_bey...@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@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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