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

Alan alanwilter at gmail.com
Tue Aug 19 11:55:05 CEST 2008

Thanks Justin for your reply.

In fact I did look that references and discussion you mentioned and actually
my e-mail was induced by them because I wanted to put some conclusions in a
straight bottom line. I've been even reading Amber manual about their
implementation for pressure and temperature coupling.

I believe that some of my questions should be only answered by running
several simulation with different approachs by myself but I also would like
to listen other's experience.

Unfortunately, wrong experiments never are published :-), and I've done
wrong simulations before and I want to avoid now.

I mean, for example for temperature coupling, that I probably should do one
bath for water + ions and another bath protein + ligand, and if Berendsen or
other, it wouldn't matter since I want to see nonbonded interactions between
ligand + protein.


> Message: 4
> Date: Mon, 18 Aug 2008 07:26:02 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] temperature coupling for
>        complex+ligand+water+ions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <48A95C4A.3000207 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 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.
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