[gmx-developers] Using PME-Switch with Thermodynamic Integration

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Thu Jan 10 19:19:36 CET 2013

If it is put in Redmine, WITH files that cause the problem, I will commit to
taking a look this Saturday at the latest to check to see if it affects 4.6.
If so, I will commit to finding a bug fix. If not, and its just a 4.5
problem, I will investigate how much work it takes to backport the solution
to 4.5. but that might take longer than this weekend.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Thu, 10 Jan 2013 19:15:08 +0100
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Using PME-Switch with Thermodynamic Integration
> On 2013-01-10 17:13, tap290 wrote:
>> Dear all,
>> I am using Gromacs to run a TI calculation to study an amino acid mutation.
>> I found that the Coulomb-short range energy (Coulomb-SR) term when TI was
>> turned on with a lambda value of 0.0 was not the same as when TI was turned
>> off. In order to determine if it was a topology problem I ran the same
>> system with a standard topology file of state A with the same coordinate
>> file with the dummy atoms removed. The Coulomb-SR interaction for the
>> standard topology agreed with the results from the dual topology when TI was
>> turned off. After various tests with the TI parameters it was discovered the
>> problem was with the PME-Switch method. When PME or Cut-off was used the
>> Coulomb-short range energy agreed. Has anyone encountered this problem
>> before?
>> I have a .tar.gz file with the directory of the problems that I can e-mail
>> to anyone if he/she needs it.
> Can you please generate a redmine issue?
> http://redmine.gromacs.org
>> Sincerely,
>> Tom Purcell
>> --
>> View this message in context:
>> http://gromacs.5086.n6.nabble.com/Using-PME-Switch-with-Thermodynamic-Integra
>> tion-tp5004457.html
>> Sent from the GROMACS Developers Forum mailing list archive at Nabble.com.
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> -- 
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