> 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. > > 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? >
Sorry, let me clarify. I was not that clear on the difference between settle and shake. The issue is that I am using SETTLE to constrain the water and I am only getting distances right to 1e-6 though I am running in double precision. David > Berk > > >> >> > >> > Thanks, >> > David >> > _______________________________________________ >> > gmx-users mailing list [email protected] >> > 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 [email protected]. >> > 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. >> [email protected] [email protected] http://folding.bmc.uu.se >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
