On 2/12/18 3:09 PM, farial tavakoli wrote: First, please note that this line is not doing anything:
define = -DUSE_OLD_C3
If you're trying to use the old CHARMM36 parameters, and not CHARMM36m, the correct keyword is -DUSE_OLD_C36. We only included that in the case that people wanted to do force field comparisons, because for folded proteins, C36 and C36m are almost identical by virtue of how we did the reparametrization.
but when I checked nvt.gro by VMD , viewed the receptor and ligand went out of the box, almost completely and ligand was separated from the protein, completely. Is there anyone who can help me and advice me why it was happened?
Sounds like a typical PBC imaging issue. Just use trjconv. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
