[gmx-users] Pressure using solvation shell

[Justin Lemkul]

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

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

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