Berk,
Any chance of getting a fix for 3.3.x versions also? I have several
papers which probably are affected by this problem and I will need to
repeat the calculations with a fixed version and produce errata. I
would prefer to do this with 3.3.x since (a) not all of the data is
with TIP4P, and so I don't need to repeat all the calcs, and would
like to use a consistent version, and (b) I am not sure that 4.x does
not introduce additional bugs that might affect my calcs.
Thanks!
David
On Jan 29, 2009, at 4:21 AM, Berk Hess wrote:
Hi,
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.
Berk
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