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

[Brett]

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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