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'Ingénierie des Systèmes Macromoléculaire (LISM) CNRS - UMR7255 31, Chemin Joseph Aiguier 13402 cedex 20 Marseille France 2016-11-28 11:17 GMT+01:00 Diogo Vila Viçosa <[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].
