[gmx-users] Re: gmx-users Digest, Vol 53, Issue 81

[sudheer babu]

 <http://www.gromacs.org/mailman/listinfo/gmx-users>

>
> Thanks to Jochen
>
   To increase the lipid molecule number from 128(which downloaded from
Dr.Tieleman site) to more than 158, I issued this command
   genbox -cs 128popc.gro -o out.gro -box 9.2 9.2 6.3 but in the output file
it showed unequal  amount water molecules on both leaflets, I have tried in
changing the box values in many ways but I couldnt able to get.
   Can any tell me how can I solve this problem to get increase in popc
molecules with equal amount of water on both leaflets.
Thanks in advance.

>
>
>
> I guess that depends on the size of your protein. You should have enough
>  lipds such that the protein doesn't interact with its preriodic image.
> 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I
> usually had something like 270 POPE molecules, but if you simulate a
> smaller protein, less lipids may be sufficient. You may also want to use
> a hexagonal box which will allow you have less lipids and water.
>
> cheers, jochen
>
> sudheer babu wrote:
> > Hi gmx-users,
> > whats the number of POPC molecules should be there after inserting
> protein
> > into popc? In my case 90 popc molecules are there around the protein from
> > 128 molecues which I downloaded from Dr.Tielman's website.
> >
> > Any suggestion will be appreciated
> > Thanks in advance.
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> >
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
> ************************************************
>
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> End of gmx-users Digest, Vol 53, Issue 81
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