Justin Lemkul wrote > Depends on the algorithm. Pressure is a fickle metric (see > http://www.gromacs.org/Documentation/Terminology/Pressure and previous > discussions on this list). It is generally advisable to run equilibration > using weak coupling (i.e. Berendsen) methods, then switch to a more robust > thermostat and barostat for further equilibration and data collection. > > -Justin
Thanks for the explanations, Justin. Talking of thermostats, after some reading I realized (correct me please if I miss something), that Nose-Hoover and V-rescale are similar in a sense they introduce corrections into kinetic energies (though they use different approaches). From this prospective, is there any preference for any of them for a simple protein-water system? I am asking because in some publications they recommend Nose-Hoover as the only alternative to simple Berendsen, but when I tried to use it in production MD I got a warning on incompatibility of Nose-Hoover with a leap-frog integrator, so it switched to a different mode. It doesn't seem to be a real problem, but since you used V-rescale for both NPT and production in your tutorial on lysozyme, I think you had certain reason for that. Thank you. -- View this message in context: http://gromacs.5086.n6.nabble.com/High-density-after-NPT-tp5003950p5003992.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
