[gmx-users] Negative pressure in NVT simulation

[Justin Lemkul]

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."

http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#non-equilibrium-md

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 
frozen.

-Justin

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

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