[gmx-users] free energy with TIP4P bug fixed

Berk Hess gmx3 at hotmail.com
Thu Jan 29 11:21:41 CET 2009


The Coulomb energy difference that Chris Neale observed recently
was caused by a bug in the neighborlist assignment with the combination
of free energy and tip4p water optimization.
This bug would cause a few tip4p-tip4p charge interactions to be missing.
I think it has been present in all Gromacs version which have tip4p optimized loops,
for sure it was in 3.3.
I have fixed this for the upcoming Gromacs 4.0.4 release.

I assume this bug also caused the cut-off dependence that David Mobley observed.

I have done a lot of free energy calculation with tip4p and never noticed
any problems. This was because I always had the perturbed molecule
in a separate energy group, which circumvents the problem.

So for the moment and for checking if you had the problem with older Gromacs 
versions, you can simply put the perturbed atoms and tip4p in separate energy groups.


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