On Fri, 2008-09-19 at 20:35 +0400, DimitryASuplatov wrote: > Hello, > could you explain my the secret of choosing to time step for md > integrator? I want to perform a 10-20 ns simulation in water in order > to, for ex., calculate some interactions or to see if the structure > would relax to a stable state. > If I use vsites, heavyh and LINCS I can run with 6 fs step. This would > be quite quick. > I just wonder if this is `by book`. > I appreciate your help. > SDA
Turn off any thermostats you have on (perform an NVE run) and then try out short runs (say, 5000 steps) with different time steps. Plot out the total energy graphs for the different runs. If your time step is too big you'll end up with total energy either increasing or decreasing. With a very big time step you might end up with an exploding system.. If you use constraints you are able to use larger time steps. With hydrogen bond length constraints the time step is about 2 fs, if the molecules are flexible the time step needs to be a lot smaller, since hydrogen atoms oscillate very fast because of their small mass. -- ------------------------------------------------------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto [EMAIL PROTECTED], p. 191 50623 ------------------------------------------------------ Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland [EMAIL PROTECTED] ------------------------------------------------------ _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
