Thank you all. I used v-rescale thermostat as following options for NVT and NPT equilibration. From the manual, v-rescale needs to set the random seed with *ld-seed*. This thermostat works correctly even for *tau-t = 0*. Are the following options correct?
*For NVT:* tcoupl = v-rescale tc_grps = PROT MEMB SOL_ION tau_t = 0 0 0 ref_t = 298 298 298 ld-seed = -1 *For NPT:* tcoupl = v-rescale tc_grps = PROT MEMB SOL_ION tau_t = 1.0 1.0 1.0 ref_t = 298 298 298 ld-seed = -1 Best regards, Mijiddorj > ------------------------------ > > Message: 5 > Date: Mon, 28 Nov 2016 13:20:13 +0000 > From: Mark Abraham <[email protected]> > To: [email protected] > Subject: Re: [gmx-users] The Berendsen thermostat does not generate > the correct kinetic energy distribution. > Message-ID: > <CAMNuMARVp5WPou6aMi0QUt-uhYn8JSdYeE-iHk8=cy1T9t45bQ@ > mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi, > > Almost right. The behaviour of the Bussi v-rescale thermostat is equivalent > to Berendsen when the system is far from equilibrium, but has the right > distribution when it is in equilibrium (see discussion in Bussi's paper in > Diogo's first link). I know of no case where Berendsen works better than > v-rescale, so you may as well use it for both equilibration and production. > (Note that old literature referring to velocity-rescaling thermostats is > talking about something totally different.) > > Mark > > On Mon, Nov 28, 2016 at 11:26 AM Marlon Sidore <[email protected]> > wrote: > > > Berendsen does not generate the correct energy distribution but > eliminates > > fluctuations faster than v-rescale. That's why it is usually used during > > equilibration. > > You might want to switch to v-rescale for your production run (I'm not > > sure, but the mdp files you got from charmm-gui probably already use > > v-rescale for the production run). > > > > Marlon Sidore > > > > > > PhD Student > > Laboratoire d'Ing?nierie des Syst?mes Macromol?culaire (LISM) > > CNRS - UMR7255 > > 31, Chemin Joseph Aiguier > > 13402 cedex 20 Marseille > > France > > > > > > 2016-11-28 11:17 GMT+01:00 Diogo Vila Vi?osa <[email protected]>: > > > > > I guess the best way to understand it is to read the original works: > > > > > > http://dx.doi.org/10.1063/1.448118 > > > http://dx.doi.org/10.1063/1.2408420 > > > > > > And try to understand the differences between the two. Afterwards, you > > > should be able to make a choice suitable for your case. > > > > > > Best, > > > Diogo > > > > > > On Mon, Nov 28, 2016 at 4:48 AM Mijiddorj Batsaikhan < > > > [email protected]> > > > wrote: > > > > > > > Dear gmx users, > > > > > > > > I want to simulation peptide on membrane. Initial structure was > created > > > by > > > > Charmm-gui, and Charmm-gui gave appropriate mdp files. I have a > > question > > > > about grompp's note. > > > > > > > > After energy minimization, I want to NVT equilibration, and grompp > gave > > > me > > > > one note as a following > > > > > > > > ****** > > > > The Berendsen thermostat does not generate the correct kinetic > energy > > > > distribution. You might want to consider using the V-rescale > > > thermostat. > > > > ****** > > > > > > > > How is V-rescale thermostat useful for the simulation? > > > > > > > > > > > > Mijiddorj > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to [email protected]. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to [email protected]. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 101 > ******************************************************* > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
