[gmx-users] heat exchanges

Berk Hess gmx3 at hotmail.com
Thu Feb 5 15:33:24 CET 2009 



> From: x.periole at rug.nl
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] heat exchanges
> Date: Thu, 5 Feb 2009 15:24:28 +0100
> 
> 
> On Feb 5, 2009, at 3:17 PM, David van der Spoel wrote:
> 
> > 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.
> the problem is due to errors with berendsen bath which eats up the
> water and therefore the protein gets cooled down while it does not need.
> The separation avoid this.
> I think links/shake have similar effects.

No, this problem is not due to the Berendsen thermostat.
The integrations errors in the electrostatics have much more effect
on the water than on the protein, because the water has higher charges
and is far more mobile. No thermostat can correct for these errors,
unless you use multiple groups.
In addition the Berendsen thermostat will move energy from fast to
slow motions. This effects becomes much stronger when the thermostat
has to do a lot of scaling due to the heat generated by cut-off's.

Inaccurate constraining will remove heat from the system, but this
effect is orders of magnitude smaller than the Coulomb cut-off heating.

Berk

> >> 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
> > _______________________________________________
> > 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
> 
> _______________________________________________
> 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! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090205/68a1e600/attachment.html>

More information about the gromacs.org_gmx-users mailing list