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

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 10 19:15:08 CET 2013

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?

> Sincerely,
> Tom Purcell
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/Using-PME-Switch-with-Thermodynamic-Integration-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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