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> > 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 > ************************************************ > > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > > End of gmx-users Digest, Vol 53, Issue 81 > ***************************************** >
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