[gmx-users] free energy with TIP4P bug fixed

Berk Hess gmx3 at hotmail.com
Tue Feb 3 11:52:22 CET 2009


There are three ways to avoid this bug with free-energy and TIP4P:
Or make sure that any energy group that contains perturbed atoms
does not include any non-perturbed atoms with charges,
or use GMX_NO_SOLV_OPT (slow),
or use the fix below.


RCS file: /home/gmx/cvs/gmx/src/mdlib/ns.c,v
retrieving revision 1.149
retrieving revision
diff -r1.149 -r1.149.2.1
<  * $Id: ns.c,v 1.149 2008/08/31 07:08:18 hess Exp $
>  * $Id: ns.c,v 2009/01/29 10:08:57 hess Exp $
<     bool      bDoVdW_i,bDoCoul_i;
>     bool      bDoVdW_i,bDoCoul_i,bDoCoul_i_sol;
>             /* For TIP4P the first atom does not have a charge,
>              * but the last three do. So we should still put an atom
>              * without LJ but with charge in the water-atom neighborlist
>              * for a TIP4p i charge group.
>              * For SPC type water the first atom has LJ and charge,
>              * so there is no such problem.
>              */
>             if (iwater == esolNO)
>             {
>                 bDoCoul_i_sol = bDoCoul_i;
>             }
>             else
>             {
>                 bDoCoul_i_sol = bDoCoul;
>             }
<             if (bDoVdW_i || bDoCoul_i)
>             if (bDoVdW_i || bDoCoul_i_sol)
<                                 else if (!bDoCoul_i)
>                                 else if (!bDoCoul_i_sol)

> Date: Mon, 2 Feb 2009 18:11:16 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] free energy with TIP4P bug fixed
> 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.
> Thanks,
> Chris.
> 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
> Hi,
> 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.
> Berk
> 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
> 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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