[gmx-users] temperatrue control again

[David van der Spoel]

On Thu, 2003-03-20 at 17:54, Anton Feenstra wrote:
> B. Nick wrote:
> > Dear Eric,
> > 
> > I have attached my input parameters. Integration
> > timestep is 0.5 fs and coupling time already 0.1 ps.
> > 
> > I have also attached the beginning of the output
> > of g_traj -f traj.trr -ot
> > that shows the temperature falling down within
> > the first picoseconds.
> 
> Does g_traj take the right number of degrees of freedom into
> account? That is needed in order to calculate temperature from
> velocities. Otherwise, if you have separate temperatures for
> these groups in your energy file, you should use those.
g_traj does not. It is however just a scaling factor. Multiply the
temperature from g_traj by
(3N-Ncons)/3N


> Alternately, it might be that mdrun -rerun will re-calculate
> the proper temperatures, but I'm not sure.
> 
I don't think you can count on these being correct...

> 
> -- 
> Groetjes,
> 
> Anton
>   _____________ _______________________________________________________
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> |  _   _  ___,| K. Anton Feenstra                                     |
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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