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

[David]

On Tue, 2005-11-01 at 08:10 -0800, Tanping Li wrote:
> Devid,
> 
> Thank you very much for your reply. I used globlly
> T-coupling and pme. Now I am nervous about it.
> Firstly, I want to check the temprature of protein and
> Sol seperately. Is there any way in Gromacs to get the
> Tem of specific group, instead of calculating Tem by
> the velocity by myself?
> 

g_traj

> 
> Tanping
> 
> --- David <spoel at xray.bmc.uu.se> wrote:
> 
> > 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
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > >
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please don't post (un)subscribe requests to the
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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
> > > 
> > > 
> > > 
> > > 
> > > _______________________________________________
> > > gmx-users mailing list
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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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> > 
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> 
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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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