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

Justin Lemkul jalemkul at vt.edu
Wed Apr 13 16:37:46 CEST 2016

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?




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


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