[gmx-users] Pressure using solvation shell

Justin Lemkul jalemkul at vt.edu
Thu Mar 1 14:11:33 CET 2018

On 2/28/18 3:28 PM, Abramyan, Tigran wrote:
> Dear Gromacs Users,
> I am using a solvation shell (-shell command) around a large nucleosome system to accelerate the simulation speed, and was wondering what ensemble is suggested to run such a system in a solvation shell?
> After a few trial runs using NPT equilibration with and without constraining the solute, I noticed that NPT squeezed the system in a way that in PBC the protein is 'touching' itself in the periodic image. I see that the system pressure is close to 1 bar at the beginning of NPT at frame 0, Pressure (bar) -8.50289. Does this mean NPT can be skipped and all equilibration and production run could be run in NVT?

It sounds like you're basically simulating a droplet, which requires 
special considerations. With NPT, your box is going to behave exactly as 
you describe - it will shrink down and try to eliminate any void space, 
and you'll end up with a pseudo-crystalline system that is probably 
badly unphysical.

With a droplet, you have to worry about evaporation (e.g. the whole 
reason people started using PBC in the first place, to get a real 
condensed-phase representation). You'll likely have to employ a 
flat-bottom position restraint to keep surface waters from drifting 
away. Then you'll also have to consider if these interfacial waters 
(because they sit at a water-vacuum boundary) have any artificial 
influence on the dynamics of your solute.



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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