[gmx-users] Heat Flux and Lambda

[Berk Hess]

> Date: Fri, 3 Oct 2008 22:26:29 +0200
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Heat Flux and Lambda
> 
> Andy Shelley wrote:
> > David,
> > 
> > I looked up the euqation for the Nose-Hoover thermostat and don't 
> > understand where lambda comes from and how to use the  number of 
> > degreees of freedom to determine the heat flux of a group. Could you 
> > explain some more?
> Aha, this only works for Berendsen I would think.

The same equation might not work, but one can do something similar.

The velocities are scaled each step by lambda, which you can get with g_energy.
The heat flux per degree of freedom is therefore simply: 0.5*k_B*T*(lambda^2 - 1).
The number of degrees of freedom for temperature coupling groups is printed
somewhere at the beginning of the log file.

Berk

> > 
> > Thanks,
> > Andy
> > 
> >  > I have been reading through the mailing list and have read some
> >  > discussion that heat flux can be indicated by the value of lambda. Can I
> >  > calculate the amount of heat flux from the lambda value?
> > In principle yes. Look up the equation for the temperature coupling. You
> > will need to know the number of degrees of freedom as printed in md.log
> > file.
> >  >
> >  > Thanks,
> >  > Andy Shelley
> >  >
> >  >
> >  > ------------------------------
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> > 
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Professor of Biology
> > 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 <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org 
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> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> 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://folding.bmc.uu.se
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