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<br><br>> Date: Mon, 9 Feb 2009 12:00:52 -0600<br>> Subject: Re: [gmx-users] shake for water<br>> From: dmobley@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> > Hi,<br>> ><br>> > I don't agree.<br>> > It uses the small 1+a approximation for the square.<br>> > Also mdrun prints the rmsd determined with independent code,<br>> > which is consistent with the (correct) tolerance.<br>> <br>> Er, yes, I have not turned on SHAKE -- I'm trying to use LINCS for<br>> bonds to hydrogen within my molecule and SETTLE for the waters. Sorry<br>> for the confusion in my original note.<br>> <br>> Anyway -- any insights as to why I'd only be getting distances correct<br>> to 1e-6 with SETTLE?<br>> <br>> Thanks,<br>> David<br>> <br><br>Ah, now we are talking about something completely different.<br>Settle gets me at least 1e-10.<br>Are you sure your problem is in the water and not in the molecule with LINCS?<br>For LINCS you will need to change lincs_order to at least 8 and lincs_iter to something<br>probably something around 8.<br><br>Berk<br><br><br>> <br>> ><br>> > Berk<br>> ><br>> >> Date: Thu, 5 Feb 2009 22:41:47 +0100<br>> >> From: spoel@xray.bmc.uu.se<br>> >> To: gmx-users@gromacs.org<br>> >> Subject: Re: [gmx-users] shake for water<br>> >><br>> >> Berk Hess wrote:<br>> >> ><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<br>> >> > > > 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<br>> >> > > > 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<br>> >> > > > 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<br>> >> > > 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<br>> >> > 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>> >><br>> >> First we compute the inverse square of the shake distance dA in tt[ll]<br>> >> for each shake pair:<br>> >><br>> >> if (bFEP)<br>> >> toler = sqr(L1*ip[type].shake.dA + lambda*ip[type].shake.dB);<br>> >> else<br>> >> toler = sqr(ip[type].shake.dA);<br>> >> dist2[ll] = toler;<br>> >> tt[ll] = 1.0/(toler*tol2);<br>> >> }<br>> >><br>> >> Then in the shake iteration we compute the difference between the<br>> >> squared distances (variable diff below):<br>> >><br>> >> tx = xp[ix]-xp[jx];<br>> >> ty = xp[iy]-xp[jy];<br>> >> tz = xp[iz]-xp[jz];<br>> >> rpij2 = tx*tx+ty*ty+tz*tz;<br>> >> toler = dist2[ll];<br>> >> diff = toler-rpij2;<br>> >><br>> >> Now we multiply the diff with tt[ll], in other words we get<br>> >> iconv = (1-rpij2/dist2)/(2 tol)<br>> >><br>> >> /* iconv is zero when the error is smaller than a bound */<br>> >> iconv = fabs(diff)*tt[ll];<br>> >><br>> >> In other words, the tolerance operates on the squared distance.<br>> >><br>> >><br>> >><br>> >><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<br>> >> > 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<br>> >> > > 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<br>> >> > 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>> >> > Express yourself instantly with MSN Messenger! MSN Messenger<br>> >> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> >> ><br>> >> ><br>> >> > ------------------------------------------------------------------------<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<br>> >> > 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>> > ________________________________<br>> > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > ________________________________<br>> > See all the ways you can stay connected to friends and family<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>> 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? 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