[gmx-users] Re: free energy with TIP4P bug fixed

David Mobley 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:

> 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
> What can you do with the new Windows Live? Find out

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