Berk, > Ah, now we are talking about something completely different. > Settle gets me at least 1e-10. > Are you sure your problem is in the water and not in the molecule with > LINCS? > For LINCS you will need to change lincs_order to at least 8 and lincs_iter > to something > probably something around 8.
I am using trjconv with -ndec to output the coordinates to gro files to 12 decimal places, then computing the distances between the atoms in the water from these coordinates. So yes, I am sure I am looking at the water molecules. The distances in question are only right to ~1e-6. Should I send input files? Thanks, David > Berk > > >> >> > >> > Berk >> > >> >> Date: Thu, 5 Feb 2009 22:41:47 +0100 >> >> From: sp...@xray.bmc.uu.se >> >> To: gmx-users@gromacs.org >> >> Subject: Re: [gmx-users] shake for water >> >> >> >> Berk Hess wrote: >> >> > >> >> > >> >> > > Date: Thu, 5 Feb 2009 19:35:09 +0100 >> >> > > From: sp...@xray.bmc.uu.se >> >> > > To: gmx-users@gromacs.org >> >> > > Subject: Re: [gmx-users] shake for water >> >> > > >> >> > > David Mobley wrote: >> >> > > > All, >> >> > > > >> >> > > > A quick question on constraints... I'm using TIP4P-Ew in gromacs >> >> > > > 3.3.2 >> >> > > > and am concerned with reproducing energies from another code very >> >> > > > precisely for several specific snapshots. I am doing a zero-step >> >> > > > mdrun >> >> > > > of a setup with one small molecule and two tip4p-ew water >> >> > > > molecules. >> >> > > > >> >> > > > Anyway, I have set the shake tolerance to 1e-12 in the mdp file, >> >> > > > but >> >> > > > to my surprise the internal water distances are good only to >> >> > > > 1e-06 >> >> > > > and >> >> > > > 1e-07. Is this expected behavior? Note that I am running in >> >> > > > double >> >> > > > precision. I assumed that, er, the distances should converge to >> >> > > > the >> >> > > > shake tolerance. >> >> > > Well, the documentation might be lacking, but the code tells the >> >> > > truth. >> >> > > It seems that the tolerance is used on the distance squared, which >> >> > > is >> >> > > consistent with your observation of a precision of 1e-6. So try >> >> > > 1e-24. >> >> > >> >> > No, it is not the square. >> >> > The code does a small 'a' approximation: (1+a)^2=1+2a+a^2 is approx >> >> > 1+2a. >> >> > I have also tested/benchmark shake in gromacs for my first lincs >> >> > paper >> >> > and the plincs paper and it always behaved the way I thought it >> >> > would. >> >> >> >> >> >> First we compute the inverse square of the shake distance dA in tt[ll] >> >> for each shake pair: >> >> >> >> if (bFEP) >> >> toler = sqr(L1*ip[type].shake.dA + lambda*ip[type].shake.dB); >> >> else >> >> toler = sqr(ip[type].shake.dA); >> >> dist2[ll] = toler; >> >> tt[ll] = 1.0/(toler*tol2); >> >> } >> >> >> >> Then in the shake iteration we compute the difference between the >> >> squared distances (variable diff below): >> >> >> >> tx = xp[ix]-xp[jx]; >> >> ty = xp[iy]-xp[jy]; >> >> tz = xp[iz]-xp[jz]; >> >> rpij2 = tx*tx+ty*ty+tz*tz; >> >> toler = dist2[ll]; >> >> diff = toler-rpij2; >> >> >> >> Now we multiply the diff with tt[ll], in other words we get >> >> iconv = (1-rpij2/dist2)/(2 tol) >> >> >> >> /* iconv is zero when the error is smaller than a bound */ >> >> iconv = fabs(diff)*tt[ll]; >> >> >> >> In other words, the tolerance operates on the squared distance. >> >> >> >> >> >> >> >> >> >> > >> >> > The problem is not that you need more iterations than 1000? >> >> > >> >> > And why not use settle that does it right at full precision at once? >> >> > >> >> > Berk >> >> > >> >> > >> >> > > >> >> > > > >> >> > > > Thanks, >> >> > > > David >> >> > > > _______________________________________________ >> >> > > > gmx-users mailing list gmx-users@gromacs.org >> >> > > > http://www.gromacs.org/mailman/listinfo/gmx-users >> >> > > > Please search the archive at http://www.gromacs.org/search before >> >> > posting! >> >> > > > Please don't post (un)subscribe requests to the list. Use the >> >> > > > www interface or send it to gmx-users-requ...@gromacs.org. >> >> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > > >> >> > > >> >> > > -- >> >> > > David van der Spoel, Ph.D., Professor of Biology >> >> > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala >> >> > > University. >> >> > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: >> >> > > +4618511755. >> >> > > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> >> > > _______________________________________________ >> >> > > gmx-users mailing list gmx-users@gromacs.org >> >> > > http://www.gromacs.org/mailman/listinfo/gmx-users >> >> > > Please search the archive at http://www.gromacs.org/search before >> >> > posting! >> >> > > Please don't post (un)subscribe requests to the list. Use the >> >> > > www interface or send it to gmx-users-requ...@gromacs.org. >> >> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > >> >> > >> >> > ------------------------------------------------------------------------ >> >> > Express yourself instantly with MSN Messenger! MSN Messenger >> >> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------ >> >> > >> >> > _______________________________________________ >> >> > gmx-users mailing list gmx-users@gromacs.org >> >> > http://www.gromacs.org/mailman/listinfo/gmx-users >> >> > Please search the archive at http://www.gromacs.org/search before >> >> > posting! >> >> > Please don't post (un)subscribe requests to the list. Use the >> >> > www interface or send it to gmx-users-requ...@gromacs.org. >> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> -- >> >> David van der Spoel, Ph.D., Professor of Biology >> >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala >> >> University. >> >> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >> >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> >> _______________________________________________ >> >> gmx-users mailing list gmx-users@gromacs.org >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at http://www.gromacs.org/search before >> >> posting! >> >> Please don't post (un)subscribe requests to the list. Use the >> >> www interface or send it to gmx-users-requ...@gromacs.org. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> > ________________________________ >> > Express yourself instantly with MSN Messenger! MSN Messenger >> > ________________________________ >> > See all the ways you can stay connected to friends and family >> > _______________________________________________ >> > gmx-users mailing list gmx-users@gromacs.org >> > http://www.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/search before >> > posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
