[gmx-users] Re: free energy with TIP4P bug fixed
dmobley at gmail.com
Thu Jan 29 13:35:24 CET 2009
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.
On Jan 29, 2009, at 4:21 AM, Berk Hess wrote:
> The Coulomb energy difference that Chris Neale observed recently
> was caused by a bug in the neighborlist assignment with the
> of free energy and tip4p water optimization.
> This bug would cause a few tip4p-tip4p charge interactions to be
> 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
> 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
> versions, you can simply put the perturbed atoms and tip4p in
> separate energy groups.
> What can you do with the new Windows Live? Find out
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users