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<br><br>> Date: Thu, 5 Feb 2009 19:35:09 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] shake for water<br>> <br>> David Mobley wrote:<br>> > All,<br>> > <br>> > A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2<br>> > and am concerned with reproducing energies from another code very<br>> > precisely for several specific snapshots. I am doing a zero-step mdrun<br>> > of a setup with one small molecule and two tip4p-ew water molecules.<br>> > <br>> > Anyway, I have set the shake tolerance to 1e-12 in the mdp file, but<br>> > to my surprise the internal water distances are good only to 1e-06 and<br>> > 1e-07. Is this expected behavior? Note that I am running in double<br>> > precision. I assumed that, er, the distances should converge to the<br>> > shake tolerance.<br>> Well, the documentation might be lacking, but the code tells the truth. <br>> It seems that the tolerance is used on the distance squared, which is <br>> consistent with your observation of a precision of 1e-6. So try 1e-24.<br><br>No, it is not the square.<br>The code does a small 'a' approximation: (1+a)^2=1+2a+a^2 is approx 1+2a.<br>I have also tested/benchmark shake in gromacs for my first lincs paper<br>and the plincs paper and it always behaved the way I thought it would.<br><br>The problem is not that you need more iterations than 1000?<br><br>And why not use settle that does it right at full precision at once?<br><br>Berk<br><br><br>> <br>> > <br>> > Thanks,<br>> > David<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>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<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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