[gmx-users] heat exchanges

[David van der Spoel]

Berk Hess wrote:
> Hi,
> 
> Strictly speaking you should never have thermostats for separate parts
> of the system when those parts are coupled through potentials.
> But in practice you can have integration errors which heat or cool different
> parts of the system in different ways.
> I think that for most systems only the electrostatics treatment will have
> a significant effect. Plain Coulomb cut-off and reaction-field both produce
> large integration errors. With PME you should never need multiple 
> t-coupl groups.
> 
> The other issue is slow heat exchange between different parts of the system.
> For a protein in solvent I think this is never an issue. But for other 
> systems
> it could be. Here it is the question if your simulation is much longer
> than this exchange time or not.
> The Berendsen thermostat can produce artifacts when you have weakly
> coupled modes. but with Gromacs 4 there is no reason to use Berendsen,
> since we have v-rescale and Nose-Hoover.
> 
> I think you can always use PME, v-rescale or nose-hoover and a single
> t-coupling group.
> 
I think you are correct, but if someone does the test it can probably be 
published, if you combine it  with recommendations for an equilibration 
protocol.

> Berk
> 
> 
>  > Date: Thu, 5 Feb 2009 13:07:21 +0100
>  > From: spoel at xray.bmc.uu.se
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] heat exchanges
>  >
>  > XAvier Periole wrote:
>  > >
>  > > On Feb 5, 2009, at 11:02 AM, Carlo Camilloni wrote:
>  > >
>  > >> Dear Gromacs users,
>  > >>
>  > >> I am doing some tests with thermostats and I would like to know if
>  > >> someone has just done it. In particular:
>  > > I have not done systematic tests but here are my impressions
>  > >>
>  > >> 1) How big has to be a protein to be coupled with a separate bath?
>  > > a few residues ...
>  > >>
>  > >> 2) Do you know over which time scales a flux of heat is observed
>  > >> between protein and solvent using only one temperature group?
>  > > few 10-100 ps.
>  > This depends a lot on how the rest of the setup is, I would think. I had
>  > some correspondence on the computational chemistry list about this 10
>  > years ago, and there people boldly stated that with Nose Hoover there is
>  > no need for coupling separate groups at all. At the time I could not
>  > reproduce that with GROMACS, but I did not persevere it. It could also
>  > have to do with flexibility, and/or using united atoms without charges,
>  > i.e. that there is little energetic coupling between e.g. water and a
>  > hydrophobic substance.
>  >
>  > It would be worthwhile to do systematic tests with different thermostats
>  > and coupling schemes. If it turns out that the same problems exist in
>  > Nose Hoover thermostats then it is probably publishable as well.
>  >
>  >
>  >
>  > >>
>  > >>
>  > >> Thanks,
>  > >>
>  > >> Carlo Camilloni
>  > >>
>  > >> --
>  > >> Dr Carlo Camilloni
>  > >> Department of Physics, University of Milano
>  > >> via Celoria, 16 - 20133 Milano, Italy
>  > >> phone: +39-02-50317654
>  > >> carlo.camilloni at mi.infn.it
>  > >> http://merlino.mi.infn.it/~carlo
>  > >>
>  > >>
>  > >>
>  > >>
>  > >>
>  > >> _______________________________________________
>  > >> gmx-users mailing list gmx-users at gromacs.org
>  > >> http://www.gromacs.org/mailman/listinfo/gmx-users
>  > >> Please search the archive at http://www.gromacs.org/search before
>  > >> posting!
>  > >> Please don't post (un)subscribe requests to the list. Use thewww
>  > >> interface or send it to gmx-users-request at gromacs.org.
>  > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>  > >
>  > > _______________________________________________
>  > > gmx-users mailing list gmx-users at gromacs.org
>  > > http://www.gromacs.org/mailman/listinfo/gmx-users
>  > > Please search the archive at http://www.gromacs.org/search before 
> posting!
>  > > Please don't post (un)subscribe requests to the list. Use thewww
>  > > 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
>  > http://www.gromacs.org/mailman/listinfo/gmx-users
>  > 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
> 
> ------------------------------------------------------------------------
> Express yourself instantly with MSN Messenger! MSN Messenger 
> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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