Dear All, If the issue in my production MD was caused by "Periodic_Boundary_Conditions", I can continue my production MD until it completed, and it will not affect my final results suppose I have it corrected by trjconv, right?
Brett At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/13/16 10:30 AM, Brett wrote: >> Dear All, >> >> >> After energy minimization and equilibrations, I am now running a 50 ns >> production MD, for a protein of 6 identical subunits, with each subunit about >> 300 residues (from resi 120 to resi 420), and there were no breaks in any >> chain. Every day it runs about 1 ns, and every day I use the command trjconv >> to get a new PDB based on the md_0_1.trr file, for the comparison between the >> new pdb and the initial pdb. >> >> >> Today I got the PDB at 6 ns. However when I checked it my pymol, I find there >> is something very strange. Although the rmsd between the 6 ns md PDB and 0ns >> md PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom >> away from this residues neighbouring residues, and correspondingly make chain >> B has a break at residue 366-367! >> >> >> Will you please let me know what is wrong with my MD, and why 2 residues >> (resi 366-367) moved 180 angstrom away? Does this phenomenon often occur? >> > >http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > >-Justin > >-- >================================================== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >================================================== >-- >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. -- 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.