[gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
Neda Rafiee
nerafiee at ipm.ir
Mon Jul 16 09:07:15 CEST 2018
Dear Justin,
I added the following energy exclusion pairs to my mdp file. Now potential energy decreased significantly but still I have a very large negative pressure (minus 10 to power 28) in my system. It seems that pressure is the same as before.Should I do anything else?
energygrp-excl= SIB SIB SIB OXB SIB OMB SIB SiSil SIB OSil SIB SiGem SIB OGem OXB OXB OXB OMB OXB SiSil OXB OSil OXB SiGem OXB OGem OMB OMB OMB SiSil OMB OSil OMB SiGem OMB OGem SiSil SiSil SiSil OSil SiSil SiGem SiSil OGem OSil OSil OSil SiGem OSil OGem SiGem SiGem SiGem OGem OGem OGem
Thanks
Neda
----- Original Message -----
From: Neda Rafiee <nerafiee at ipm.ir>
To: gmx-users at gromacs.org
Sent: Mon, 16 Jul 2018 00:01:35 +0430 (IRDT)
Subject: [Spam-FG][gmx-users] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation
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<PRE>
Dear Justin,
Thanks a lot for your response.
Neda
----- Original Message -----
From: Justin Lemkul
To: gmx-users at 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 at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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