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Hi,<br><br>There are three ways to avoid this bug with free-energy and TIP4P:<br>Or make sure that any energy group that contains perturbed atoms<br>does not include any non-perturbed atoms with charges,<br>or use GMX_NO_SOLV_OPT (slow),<br>or use the fix below.<br><br>Berk<br><br>RCS file: /home/gmx/cvs/gmx/src/mdlib/ns.c,v<br>retrieving revision 1.149<br>retrieving revision 1.149.2.1<br>diff -r1.149 -r1.149.2.1<br>3c3<br>< * $Id: ns.c,v 1.149 2008/08/31 07:08:18 hess Exp $<br>---<br>> * $Id: ns.c,v 1.149.2.1 2009/01/29 10:08:57 hess Exp $<br>544c544<br>< bool bDoVdW_i,bDoCoul_i;<br>---<br>> bool bDoVdW_i,bDoCoul_i,bDoCoul_i_sol;<br>956a957,971<br>> /* For TIP4P the first atom does not have a charge,<br>> * but the last three do. So we should still put an atom<br>> * without LJ but with charge in the water-atom neighborlist<br>> * for a TIP4p i charge group.<br>> * For SPC type water the first atom has LJ and charge,<br>> * so there is no such problem.<br>> */<br>> if (iwater == esolNO)<br>> {<br>> bDoCoul_i_sol = bDoCoul_i;<br>> }<br>> else<br>> {<br>> bDoCoul_i_sol = bDoCoul;<br>> }<br>958c973<br>< if (bDoVdW_i || bDoCoul_i)<br>---<br>> if (bDoVdW_i || bDoCoul_i_sol)<br>1031c1046<br>< else if (!bDoCoul_i)<br>---<br>> else if (!bDoCoul_i_sol)<br><br><br>> Date: Mon, 2 Feb 2009 18:11:16 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] free energy with TIP4P bug fixed<br>> <br>> Hi Berk,<br>> <br>> Could you please post the relevant cvs diff here? While my energies are now output consistently for zero-step mdruns while separating <br>> my energygrps, I am still seeing some very aberrant behaviour when I apply the free-energy code during a 2-10 ns MD run, <br>> 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 <br>> or instead utilize the couple-moltype mdp options.<br>> <br>> 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 <br>> as this is beginning to take some time.<br>> <br>> Thanks,<br>> Chris.<br>> <br>> From: gmx3 at hotmail.com <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> To: gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> Subject: RE: [gmx-users] Re: free energy with TIP4P bug fixed<br>> Date: Thu, 29 Jan 2009 13:48:20 +0100<br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> Hi,<br>> <br>> You can apply the cvs diff.<br>> But even simpler, as I said, is just putting your solute and solvent in separate charge** groups.<br>> <br>> ** I meant separate energy groups.<br>> <br>> This should circumvent the issue.<br>> <br>> Berk<br>> <br>> From: dmobley at gmail.com <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> To: gmx3 at hotmail.com <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> Date: Thu, 29 Jan 2009 06:35:24 -0600<br>> CC: gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users><br>> Subject: [gmx-users] Re: free energy with TIP4P bug fixed<br>> <br>> Berk,<br>> 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.<br>> Thanks!David<br>> On Jan 29, 2009, at 4:21 AM, Berk Hess wrote:Hi,<br>> <br>> The Coulomb energy difference that Chris Neale observed recently<br>> was caused by a bug in the neighborlist assignment with the combination<br>> of free energy and tip4p water optimization.<br>> This bug would cause a few tip4p-tip4p charge interactions to be missing.<br>> I think it has been present in all Gromacs version which have tip4p optimized loops,<br>> for sure it was in 3.3.<br>> I have fixed this for the upcoming Gromacs 4.0.4 release.<br>> <br>> I assume this bug also caused the cut-off dependence that David Mobley observed.<br>> <br>> I have done a lot of free energy calculation with tip4p and never noticed<br>> any problems. This was because I always had the perturbed molecule<br>> in a separate energy group, which circumvents the problem.<br>> <br>> So for the moment and for checking if you had the problem with older Gromacs <br>> versions, you can simply put the perturbed atoms and tip4p in separate energy groups.<br>> <br>> Berk<br>> <br>> <br>> What can you do with the new Windows Live? Find out<br>> <br>> See all the ways you can stay connected to friends and family<br>> _________________________________________________________________<br>> Express yourself instantly with MSN Messenger! Download today it's FREE!<br>> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090129/1179cae4/attachment-0001.html<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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