[gmx-users] Negative pressure in NVT simulation

Justin Lemkul jalemkul at vt.edu
Sun Jul 15 20:39:23 CEST 2018

On 7/15/18 2:32 PM, Neda Rafiee wrote:
> ;
> energygrps          = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW
> energygrp_table = NaB OXB NaB OSil NaB OGem NaB OMB OMB OW OW SIB OW SiSil OW SiGem OW HSil OW HGem HW OMB HW OXB OW OSil OW OGem HW OSil HW OGem OXB OW
> freezegrps          = SIB OXB OMB SiSil OSil SiGem OGem
> freezedim           = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y

You're not using energy group exclusions, which the manual recommends 
when freezing:

"To avoid spurious contributions to the virial and pressure due to large 
forces between completely frozen atoms you need to use energy group 
exclusions, this also saves computing time."


Freezing is a very severe artificial perturbation, so you will have to 
use hacks like that if you intend to do a simulation with so many things 



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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