[gmx-users] Re: temperature coupling for complex+ligand+water+ions
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 19 13:34:55 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.
Well, the choice is yours, and I guess will depend largely on how sensitive you
think your system might be to obtaining an accurate statistical ensemble. The
discussion on the list opened my eyes to a lot of new ideas. Using Berendsen
seems to have become de facto among most users (after all, the paper has been
cited almost 6,000 times). After doing a lot of reading (thanks to all who
posted references), I have begun simulating using Nose-Hoover with two groups
(i.e., Protein Non-protein), as I have found some references that suggest this
approach and have acquired good results.
As long as you can justify whatever you're doing, I guess you should go ahead.
But that justification can be tricky, depending on who you talk to :)
> Message: 4
> Date: Mon, 18 Aug 2008 07:26:02 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] temperature coupling for
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <48A95C4A.3000207 at vt.edu <mailto: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:
> 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.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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