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 :)
-Justin
Cheers,
Alan
Message: 4
Date: Mon, 18 Aug 2008 07:26:02 -0400
From: "Justin A. Lemkul" <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
Subject: Re: [gmx-users] temperature coupling for
complex+ligand+water+ions
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
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
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Virginia Tech
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