Hi, I would like to simulate protein in DMPC bilayer in Charmm36 ff. I checked mailing list and KALP-15 tutorial, but still I have a few basic questions.
1) I have problem with DMPC bilayer... - VMD membrane builder only provides POPE and POPC lipids... - on the Peter Tieleman page there is a pdb but with different atom names and without H, of course I can rename atoms but pdb2gmx would not regenerate hydrogens - lipids.hdb file is empty - I have found also this page: http://terpconnect.umd.edu/~jbklauda/research/download.html and it works but I am not able to extend bilayer with genconf... I always end up with separated copies of starting patch... even with -dist 0 0 0. 2) How to choose proper lipid patch size and simulation box size? For globular proteins I would just run editconf with -bt dodecahedron -d 1. How it is done in membrane protein simulation? Thanks a lot for any help and suggestions. Best! tomek
-- 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
