[gmx-users] What is the difference between joined and seperate tem coupling?

[David]

On Tue, 2005-11-01 at 08:16 +0100, Erik Lindahl wrote:
> Hi,
> 
> If you use PME you're fine with either. If you have cut-offs and  
> large drifts in energy you run a risk of e.g. the water beeing cooler  
> than the protein if you only use global coupling.

I'm not sure this is correct. Heat exchange between components for which
the forces are relatively weak is as far as I know a problem. Please
test it and report back to the list. It may also be slightly worse for
GROMOS than for OPLS since OPLS has more charged atoms in the protein
than GROMOS.

Why don't you do four 500 ps sims with GROMOS and OPLS and with separate
coupling groups and only one, and make a table of the protein
temperatures in respective simulations. You will have to save velocities
relatively often  to compute the temperature in the simulation where you
only have one group.

> 
> Cheers,
> 
> Erik
> 
> 
> On Nov 1, 2005, at 1:28 AM, Tanping Li wrote:
> 
> > Dear all,
> >
> > I am simulating the hyrdation issume of protein under
> > NVT  condition. We use Gromos96 force field. I noticed
> > that in the tutorial mdp file, the protein and solvent
> > are tem coupled seperately. Could I use the global
> > tem-coupling? Is there any real difference between
> > them?
> > Thank you very much for your reply.
> >
> >
> > Best
> > Tanping Li
> > _______________________________________________
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> >
> 
> -----------------------------------------------------------
> Erik Lindahl  <lindahl at sbc.su.se>
> Assistant Professor, Stockholm Bioinformatics Center
> Stockholm University, SE 106 91 Stockholm
> Phone: +46 8 5537 8564     Fax: +46 8 5537 8214
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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