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

tap290 tap290 at nyu.edu
Thu Jan 10 17:13:08 CET 2013

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

I have a .tar.gz file with the directory of the problems that I can e-mail
to anyone if he/she needs it.


Tom Purcell

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