[gmx-users] temperature coupling for complex+ligand+water+ions

[Justin A. Lemkul]

Alan wrote:
> Dears,
> 
> I took a look at wikis and keep following this list but I still have 
> doubts that I would appreciate any advice for.
> 
> What would be the recommended approach for temperature coupling for a 
> system composed of protein + ligand + water + ions?
> Which termostat: Berendsen or Nose-Hoover?
> NPT by the way? Which algorithm: Berendsen or Parrinello-Rahman?
> 

There was a really interesting thread that several very knowledgeable 
individuals contributed to not too long ago; one of the first posts is here:

http://www.gromacs.org/pipermail/gmx-users/2008-July/035316.html

There are many good references provided in the thread about different coupling 
algorithms.  The original Berendsen thermostat does not correspond to any known 
ensemble, unlike some of the other methods.  I would suggest having a look at 
the references provided in that thread.

-Justin

> I am interested in protein/ligand interactions.
> 
> Many thanks in advance.
> Cheers,
> Alan
> -- 
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>  >>http://www.bio.cam.ac.uk/~awd28<<
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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