I am not sure where the idea of using berendsen barostat with the v-rescale thermostat for equilibration came from, however. Doesn't the typical equilibration begin with v-rescale for temperature equilibration then adding parinello-rahman barostat then switching to nose-hoover for production runs (as nose-hoover chains result in the correct canonical distribution)?
On 2012-09-19 04:24:27PM -0700, Ladasky wrote: > Dear Sara, > > I just had a problem with my simulations that I traced to the use of the > V-rescale temperature algorithm. Here is my recent post: > > http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121 > > V-rescale may be appropriate in certain simulations, but it is apparently > NOT appropriate when used with Berendsen pressure coupling during the > initial equilibration. I don't know if that is related to your problem, but > it's something that I just discovered the hard way. > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/v-rescale-tp5001066p5001122.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists