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

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 18 13:26:02 CEST 2008

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:


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.


> 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


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