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

[Tanping Li]

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?


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
> > > _______________________________________________
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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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