[gmx-users] pressure coupling error in umbrella sampling

Justin Lemkul jalemkul at vt.edu
Wed Feb 14 19:28:24 CET 2018

On 2/14/18 1:06 PM, kordzadeh at aut.ac.ir wrote:
> Hi Dr.Lemkul
> Thank you very much for your answer
> I get it now, before your answer I run system with -maxwarn 1, I saw trajectory in vmd , my drug molecule break in middle of run and then corrected, is it wrong?

No, that's called periodic boundary conditions.

> has it occured because using maxwran?


> is vmd an appropriate tool for detect trajectory?

You can use whatever visualization software you like, but you should use 
trjconv first to get a consistent, intact representation.

> I alaways after run, check trajectory with vmd to sure in time of simulation all structure were complete.

VMD is good for visualizing and some analysis, but it's not going to 
tell you anything about the physical validity of your simulation or the 
methods you used. That's what grompp was warning you about in the first 
place. If the simulation finished, there was likely no problem; the 
warning is intended to tell you that things *may* be unstable with 
Parrinello-Rahman if you are simultaneously generating velocities.

> I will do your advise, and I will run with Benedsen probably it will solve my problem

The "broken" molecule is not a problem and will not be magically solved 
by using a different barostat.



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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