Hi Ricardo, If you've generated your membrane without taking PBC into account, then I'd say measuring the extent and setting the box manually (editconf -box) is the best option you have.
Cheers, Tsjerk On Thu, Feb 16, 2012 at 5:44 PM, Ricardo O. S. Soares <[email protected]> wrote: > Hello dear users, > > I'm familiar with solvated protein simulations for quite a while now. > Recently I'm beginning to study some membrane systems. > I have created a POPC membrane and now I need to make a proper box. Using > editconf, the box is always larger than the membrane's x and y coordinates, > even controlling the -d option. > I could measure the membrane and set the box values manually, but that > doesn't seem to me to be a safe approach. > I read Justin Lemkul's tutorial on membranes, and I see that there were > already a box in the downloaded file, so I couldn't figure something out > from there yet. > > Thanks > > > > > > > > --- > > Ricardo O. S. Soares , PhD Student. > Group of Biological Physics - Department of Physics & Chemistry > Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São > Paulo. > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
