[gmx-users] [Spam-FG] [Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

Neda Rafiee nerafiee at ipm.ir
Mon Jul 16 09:33:50 CEST 2018 

Dear Mark,
Thanks a lot for your useful suggestions
Neda


----- Original Message -----
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Sent: Mon, 16 Jul 2018 11:49:38 +0430 (IRDT)
Subject: Re: [gmx-users] [Spam-FG]	[Spam-FG]__Re:_[Spam-FG]_Re:__Negative_pressure_in_NVT_simulation

Hi,

I presume that's because you still have interactions between groups that
are frozen.

You can make your life easier by using only the groups you need for your
simulation, e.g. those needing a table and those that are frozen. If you
are trying to get per-residue decomposition, then (first) make sure your
force field was parametrized such that this is meaningful (most aren't),
and prefer to do that analysis using mdrun -rerun. mdrun goes slower for
each energy group that has interactions to compute, so minimize that.

I would also have done a simulation with just my slab and found this
pressure issue back then. It is good practice to add complexity to models
incrementally, after validating your expectations on the simulation at the
previous stage.

Mark

On Mon, Jul 16, 2018 at 9:07 AM Neda Rafiee <nerafiee at ipm.ir> wrote:

> 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]
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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:
> &gt; ;
> &gt; energygrps          = LYS LEU VAL PHE1 PHE2 ALA GLU ASP NaB ClB OXB
> OSil OGem OMB SIB SiSil SiGem HSil HGem OW HW
> &gt; 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
> &gt;
> &gt; freezegrps          = SIB OXB OMB SiSil OSil SiGem OGem
> &gt; freezedim           = Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y Y
>
> You&#39;re not using energy group exclusions, which the manual recommends
> when freezing:
>
> &quot;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.&quot;
>
>
> 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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