On 7/30/13 3:02 PM, S. Alireza Bagherzadeh wrote:
On Tue, Jul 30, 2013 at 7:04 AM, <gmx-users-requ...@gromacs.org> wrote:
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Today's Topics:
1. generating user-defined topologies for surfaces (Valentina)
2. Re: generating user-defined topologies for surfaces
(Justin Lemkul)
3. Re:
energy conservation / frozen atoms (Justin Lemkul)
4. Re: generating user-defined topologies for surfaces (Valentina)
5. Re: generating user-defined topologies for surfaces (Valentina)
6. Re: Re: generating user-defined topologies for surfaces
(Justin Lemkul)
------------------------------
Message: 3
Date: Tue, 30 Jul 2013 07:20:53 -0400
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] energy conservation / frozen atoms
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <51f7a195.80...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 7/29/13 10:51 PM, S. Alireza Bagherzadeh wrote:
Hi All,
I am simulating a system in which I have two solid surfaces and I keep
them
frozen during simulations. I also exclude the interactions between its
atoms to avoid spurious contribution to the virial pressure due to large
forces between them as suggested in the manual.
I run a nvt for equilibration and then I do the production run in an nve
ensemble; however, I am not getting good energy conservation. There is a
huge energy drift...
When I remove the solid surfaces, I will only have water molecules and
united atom methane molecules in my system. Using the same protocol I
obtain a very good energy conservation...
What happens if you unfreeze the frozen surfaces and run the same system?
The point is I do not want to do this as I am trying to save some
calculations.
My point in asking is to do some diagnostics. There are countless similar posts
to yours - freeze some group(s), energy conservation is bad, and then a dead end
to the thread. It would be interesting, from a development standpoint, to know
whether the issue is truly linked to the frozen group(s). Using strong position
restraints in lieu of frozen groups is probably a reasonable workaround that
could also be used to find a problem.
My system is already big and including all of the bond, angles and dihedral
interactions of the solid surfaces slows down the simulation considerably.
The bonded interactions are not likely what slows the system down. Freezing
doesn't actually improve performance. Using energygrp_excl is what causes a
speed-up.
Any insight on what might be wrong in my system would be very
appreciated.
The contents of the .edr file will probably be informative, as you can
identify
which energy term(s) is(are) most affected. It's all probably related to
the
frozen surfaces themselves acting as an energy sink or something.
Is there anyway to fix the "energy sinking" effect of the surfaces?
That's just an off-the-cuff guess at something being wrong. Like I said above,
there's been no thorough evaluation of whether or not this sort of combination
does (or should) work.
I used dl_poly to simulate a similar system and there was no problem with
the energy conservation.
That's been reported before, hence something is probably wrong with Gromacs, but
we need more information to figure it out and fix it. Otherwise, you'll have to
figure out an alternate strategy.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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