I've done some extensive testing (paper on testing method in the works) and vrescale gives a very accurate ensemble very well for NVT. Parrinello-Rahman and MTTK are the only algorithms that are correct for NPT. Berendsen barostat is not. Note that there is a bug with vrescale + md-vv + that is fixed in 4.6 and (hopefully) for the next patch of 4.5.
For equilibrating a system, Berendsen for both temperature and pressure is the best bet. They artificially minimize fluctuations, which is great for equilibration, bad for data collection. On Thu, Sep 20, 2012 at 6:05 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 20/09/2012 9:35 AM, Peter C. Lai wrote: >> >> 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)? > > > N-H does have known issues, see > http://link.aip.org/link/doi/10.1063/1.2989802 and > http://link.aip.org/link/doi/10.1063/1.2408420. I am not aware of any > shortcomings of the Bussi v-rescale thermostat in GROMACS. > > Mark > > >> >> 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 > > > -- > 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 -- 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
