[EMAIL PROTECTED] wrote: >> 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. > > A hexagonal box? Great. How does one go about constructing that? Is this > a cylinder-like box with hexagonal shape or just a triclinic one? In the > triclinic case, does the PBC membrane turn out as it should?
And yes, the PBCs work just fine, as expected from any triclinic box. cheer, jochen > > Thanks, > Chris. > > > _______________________________________________ > 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! > Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > . > -- ************************************************ 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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php