[gmx-users] Re: free energy with TIP4P bug fixed
gmx3 at hotmail.com
Thu Jan 29 13:50:39 CET 2009
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Re: free energy with TIP4P bug fixed
Date: Thu, 29 Jan 2009 13:48:20 +0100
You can apply the cvs diff.
But even simpler, as I said, is just putting your solute and solvent in separate charge** groups.
** I meant separate energy groups.
This should circumvent the issue.
From: dmobley at gmail.com
To: gmx3 at hotmail.com
Date: Thu, 29 Jan 2009 06:35:24 -0600
CC: gmx-users at gromacs.org
Subject: [gmx-users] Re: free energy with TIP4P bug fixed
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.
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