[gmx-users] Pressure using solvation shell
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
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.
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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