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

Brett brettliu123 at 163.com
Wed Apr 13 16:30:59 CEST 2016

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.


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