[gmx-users] Pressure using solvation shell

[Abramyan, Tigran]

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,


Thanks,

Tigran


--
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