[gmx-users] Re: Question about Berendsen thermostat and
baptista at itqb.unl.pt
baptista at itqb.unl.pt
Thu Jul 24 21:46:25 CEST 2008
On Thu, 24 Jul 2008, David van der Spoel wrote:
> Michael Shirts wrote:
>>>> Thanks for the tip!
>> You're welcome!
>>>> That thermostat is really nice and also simple to implement.
>>>> It is now in CVS.
>>> If this thermostat has a stochastic term, is the dynamics still
>>> meaningful then?
>> Of course it's not! No thermostat gives physical dynamics. But at
>> least it gives the canonical distribution at equilibrium!
> Well in that case I'm not sure what is more important for me. It depends on
> the application I presume.
> But does the NH chain, the mother of all thermostats, indeed yield correct
I would say that the mother and father(!) of all thermostats and barostats
are in Andersen's 1980 paper, where he proposed both a stochastic
temperature bath and a deterministic extended-system pressure bath (latter
nicely adapted by Nose to the temperature case). As far as I know, this
was the first time that someone came out with methods that can be shown to
(asymptoticaly) sample from the proper ensembles, going beyond the simple
ad hoc velocity-scaling and similar methods previously used (the
As Michael already noted, there are really no true dynamics except in a
constant-energy method (well, if there is anything "true" in a system with
periodic boundaries...) For example, in an extended-system heat bath (eg,
Nose) only the extended system has "true" dynamics, since its trajectory
is microcanonical. And although the projection of that extended
microcanonical distribution onto the original (non-extended) space turns
out to be canonical, there is no reason why the dynamics should be
preserved after the projection. This is usually not a problem because you
often just want to get a decent canonical sampling (unless you are trying
to measure temporal properties, of course). In practice, it turns out that
you can always fiddle with the values of the time-related parameters of
the bath ("piston masses" in extended-system methods, "collision
frequencies" in stochastic methods) until you get a good temporal behavior
(though you should always keep in mind that those values may be
Besides time, we usually don't really care about velocities. Therefore, a
quite simple procedure is to keep the "instantaneous temperature" (ie,
kinetic energy) fixed using Gauss' principle of least constraint. Although
that may sound unphysical, it is easy to show from the Liouville equation
that the positions strictly follow a canonical distribution (this can be
found somewhere in one of Denis Evans' 1980's papers). As far as I
remember, there are no parameters of any sort in this isokinetic
thermostat and the equations of motion are quite simple. If anyone wants
to implement it... :)
> (I realize I should know all this, but hey...)
>> gmx-users mailing list gmx-users at gromacs.org
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, Apartado 127
2780-157 Oeiras, Portugal
phone: +351-214469619 email: baptista at itqb.unl.pt
fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista
More information about the gromacs.org_gmx-users