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

[Tanping Li]

Dear Devid,

Under pme and globlly T-coupling at 295K, I get the
tem for protein, water and Na in my system like this:

          Protein  Sol    Na
Average   293       297   434

Is it acceptable?


The tem of Na is very large. Does that tells me that
thfe charged groups in protein will also deviate far
away fro the average Tem? I am analysising the
interaction between a specific residue and close
waters. Do I need to seperately couple their tem since
I find out that tem of this specific residue(trp) is a
little bit from 295K. Thank you very much for your
help.


Tanping



--- David <spoel at xray.bmc.uu.se> wrote:

> 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
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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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> > > 
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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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