On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote: > Jussi Lehtola wrote: > > I'm experiencing trouble converging the density of some heavy liquid > > alcohols (after 10 ns of simulation the density is still changing > > linearly). Is there any way to run pressure annealing in Gromacs? > > Running the system through a high pressure and temperature might give an > > equilibrium structure quicker. > > There's nothing native that I'm aware of, but it should be > straightforward to use sed or perl in a script to do the annealing "by > hand" in a series of mdrun invocations.
Yup, that came to mind but then one ends up with N trajectories and log files. And one has to run a big pile of grompp commands, that waste some parallel run time, so I really would like something integrated. Besides, a thing like changing the reference pressure should be a no-brainer in the source code - assuming the code is well structured and one knows it well beforehand. Anyway, the problem was solved for now already. Still, pressure annealing would be a nice addon to gromacs. (I'll open a bug on bugzilla about it.) -- ------------------------------------------------------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ------------------------------------------------------ Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi ------------------------------------------------------ -- gmx-users mailing list gmx-users@gromacs.org http://lists.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
