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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Apr 14 06:16:58 CEST 2016


right!

Cheers,

Tsjerk
On Apr 14, 2016 05:32, "Brett" <brettliu123 at 163.com> wrote:

> 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" <jalemkul at 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
> >
> >jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >http://mackerell.umaryland.edu/~jalemkul
> >
> >==================================================
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