[gmx-users] pressure coupling error in umbrella sampling

Justin Lemkul jalemkul at vt.edu
Wed Feb 14 14:10:21 CET 2018

On 2/12/18 6:34 AM, kordzadeh at aut.ac.ir wrote:
> Hi Dr.Abraham
> Thank you very much for your answer
> yas I 've extacted configuration with 0.2 nm distance and when I want to run NPT for first configuration,I gave that error.
> I didn't undersatnd this mdp file for this step, I got this file from umbrella sampling tutorial and I adjusted for my system but I didn't understand
> we are doing a pullind simulation with zero velocity, I think the aim is to costriant structure by artifial spring but we don't  move it, am I right?

The application of a biasing potential (which is not a constraint) is 
separate from the technical issue of Parrinello-Rahman pressure coupling 
being applied in conjunction with generating velocities. I wrote the 
tutorial and input files years ago when grompp didn't complain about 
this. I had no problems with stability, but this may not always be the 
case. So grompp is trying to help you by pointing out that this 
particular combination of options may not be wise. You may wish to do a 
short NPT equilibration with Berendsen pressure coupling before starting 
data collection.



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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