[gmx-users] free energy with TIP4P bug fixed
bharat v. adkar
bharat at sscu.iisc.ernet.in
Tue Feb 3 16:16:00 CET 2009
dear Berk,
please let us know whether following patch is correct for 3.3.1
diff orig-ns.c ns.c
2c2
< * $Id: ns.c,v 1.84.2.3 2006/03/01 07:57:46 spoel Exp $
---
> * $Id: ns.c,v 1.84.2.3.1 2009/02/03 20:27:00 hess Exp $
617c617
< bool bDoVdW_i,bDoCoul_i;
---
> bool bDoVdW_i,bDoCoul_i,bDoCoul_i_sol;
992,993c992,1009
<
< if (bDoVdW_i || bDoCoul_i)
---
>
> /* 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_sol)
1052c1068
< else if (!bDoCoul_i)
---
> else if (!bDoCoul_i_sol)
thanks
bharat
On Tue, 3 Feb 2009, Berk Hess wrote:
>
> Hi,
>
> 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.
>
> Berk
>
> RCS file: /home/gmx/cvs/gmx/src/mdlib/ns.c,v
> retrieving revision 1.149
> retrieving revision 1.149.2.1
> diff -r1.149 -r1.149.2.1
> 3c3
> < * $Id: ns.c,v 1.149 2008/08/31 07:08:18 hess Exp $
> ---
>> * $Id: ns.c,v 1.149.2.1 2009/01/29 10:08:57 hess Exp $
> 544c544
> < bool bDoVdW_i,bDoCoul_i;
> ---
>> bool bDoVdW_i,bDoCoul_i,bDoCoul_i_sol;
> 956a957,971
>> /* 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;
>> }
> 958c973
> < if (bDoVdW_i || bDoCoul_i)
> ---
>> if (bDoVdW_i || bDoCoul_i_sol)
> 1031c1046
> < 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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