[gmx-users] Pressure using solvation shell

Abramyan, Tigran tigran at email.unc.edu
Wed Feb 28 21:28:09 CET 2018

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?

Please advise,



Tigran M. Abramyan, Ph.D.
Postdoctoral Fellow, Computational Biophysics & Molecular Design
Center for Integrative Chemical Biology and Drug Discovery
Eshelman School of Pharmacy
The University of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7363

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