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<PRE>
Dear Justin,
Thanks a lot for your response.
Neda
----- Original Message -----
From: Justin Lemkul <jalemkul@vt.edu>
To: gmx-users@gromacs.org
Sent: Sun, 15 Jul 2018 23:09:11 +0430 (IRDT)
Subject: [Spam-FG] Re: [gmx-users] Negative pressure in NVT simulation
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<PRE>
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
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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