[gmx-users] free energy with TIP4P bug fixed

Chris Neale chris.neale at utoronto.ca
Tue Feb 3 00:11:16 CET 2009

Hi Berk,

Could you please post the relevant cvs diff here? While my energies are now output consistently for zero-step mdruns while separating 
my energygrps, I am still seeing some very aberrant behaviour when I apply the free-energy code during a 2-10 ns MD run, 
even with lambda=0.0. I get the same strange behaviour whether I explicitly make a B-state with no charges in the .itp file 
or instead utilize the couple-moltype mdp options.

I will try the bash "export GMX_NO_SOLV_OPT" solution over the next few days, but I'd like to try all possible solutions in parallel 
as this is beginning to take some time.


From: gmx3 at hotmail.com <http://www.gromacs.org/mailman/listinfo/gmx-users>
To: gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
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 <http://www.gromacs.org/mailman/listinfo/gmx-users>
To: gmx3 at hotmail.com <http://www.gromacs.org/mailman/listinfo/gmx-users>
Date: Thu, 29 Jan 2009 06:35:24 -0600
CC: gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
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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