[gmx-users] very strange phenomenon for my production MD by gromacs

[Dries Van Rompaey]

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" <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.
>
>
> Brett
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