[gmx-users] Umbrella sampling

Justin Lemkul jalemkul at vt.edu
Sun Dec 3 23:24:55 CET 2017

On 12/3/17 8:01 AM, rose rahmani wrote:
> On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 11/28/17 12:23 AM, rose rahmani wrote:
>>> Hello;
>>> I took 2000 configuration from trajconv. Amino acid is in its normal shape
>>> till almost conf1000.gro(and a little more). But in for example
>>> conf1300.gro amino acid was disintegrated. What does it mean? Would you
>>> please help me?
>> Bonds can't break and molecules can't "disintegrate" - what you're seeing
>> is probably a result of PBC.
>> http://www.gromacs.org/Documentation/Terminology/Periodic_
>>> Boundary_Conditions
>> I don't know why this doesn't work since yesterday?!!!!...anyway...
> I used trjconv for just one frame for example conf2000;
> trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
> whole
> so protein turned into to its normal shape, but i'm not sure does it makes
> sense or not?! is that right? if it's right, another problem is;
>   protein is getting out of box, should i use trjconv for centering?
> Thank you for your attentions

A "whole" molecule only matters for visualization. It has no impact on 
physical interactions computed by mdrun.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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