[gmx-users] very strange phenomenon for my production MD by gromacs
Dries Van Rompaey
dries.vanrompaey at gmail.com
Wed Apr 13 16:38:07 CEST 2016
Sounds like you're experiencing periodic boundary artifacts. Take a look at
the following link:
On 13 Apr 2016 4:31 p.m., "Brett" <brettliu123 at 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.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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-request at gromacs.org.
More information about the gromacs.org_gmx-users