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

[Shirts, Michael (mrs5pt)]

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.

Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> 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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