Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me?
I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the higher the frequency, the more accurate T will be, I wonder whether it will get artifacts for in MD run.. since the warning in Gromacs says tau_t should be 20 times bigger than dt*nsttcouple.. Best, Qin 2010/12/25 David van der Spoel <sp...@xray.bmc.uu.se> > On 12/24/10 6:40 PM, ms wrote: > >> On 24/12/10 12:26, David van der Spoel wrote: >> >> I'm not an expert, but isn't Berendsen usually not used because it >>>> doesn't give a correct ensemble? I may be partial because I personally >>>> know Giovanni Bussi, but it seems from what I've heard that v-rescale is >>>> the best choice usually. >>>> >>>> V-rescale is a good choice. Berendsen not only gives you the wrong >>> ensemble but it also biases the energy distribution to lower energies. >>> >> >> Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to >> less confusion if it is removed? :) >> >> It's still useful for equilibration, e.g. gas to liquid conversion. > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > -- > 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