Hi, Sounds like you're experiencing periodic boundary artifacts. Take a look at the following link: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Dries On 13 Apr 2016 4:31 p.m., "Brett" <brettliu...@163.com> 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? > > > I am looking forward to getting a reply from you. > > > Brett > -- > 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.