[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

Alan wrote:
> 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 :)


> Cheers,
> Alan
>     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
>            complex+ligand+water+ions
>     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:
>     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


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