[gmx-users] Re: energy conservation / frozen atoms

Justin Lemkul jalemkul at vt.edu
Tue Jul 30 22:26:50 CEST 2013

On 7/30/13 3:02 PM, S. Alireza Bagherzadeh wrote:
> On Tue, Jul 30, 2013 at 7:04 AM, <gmx-users-request at 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 <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] energy conservation / frozen atoms
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <51F7A195.80404 at 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 

>>> 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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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