<div dir="ltr"><div class="gmail_quote"><div>Thanks Justin for your reply.</div><div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div>
<div>Unfortunately, wrong experiments never are published :-), and I've done wrong simulations before and I want to avoid now.</div><div><br></div><div>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.</div>
<div><br></div><div>Cheers,</div><div>Alan</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
Message: 4<br>
Date: Mon, 18 Aug 2008 07:26:02 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] temperature coupling for<br>
complex+ligand+water+ions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:48A95C4A.3000207@vt.edu">48A95C4A.3000207@vt.edu</a>><br>
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<br>
<br>
<br>
Alan wrote:<br>
> Dears,<br>
><br>
> I took a look at wikis and keep following this list but I still have<br>
> doubts that I would appreciate any advice for.<br>
><br>
> What would be the recommended approach for temperature coupling for a<br>
> system composed of protein + ligand + water + ions?<br>
> Which termostat: Berendsen or Nose-Hoover?<br>
> NPT by the way? Which algorithm: Berendsen or Parrinello-Rahman?<br>
><br>
<br>
There was a really interesting thread that several very knowledgeable<br>
individuals contributed to not too long ago; one of the first posts is here:<br>
<br>
<a href="http://www.gromacs.org/pipermail/gmx-users/2008-July/035316.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2008-July/035316.html</a><br>
<br>
There are many good references provided in the thread about different coupling<br>
algorithms. The original Berendsen thermostat does not correspond to any known<br>
ensemble, unlike some of the other methods. I would suggest having a look at<br>
the references provided in that thread.<br>
<br>
-Justin<br>
<br>
> I am interested in protein/ligand interactions.<br>
><br>
> Many thanks in advance.<br>
> Cheers,<br>
> Alan<br>
> --<br></blockquote></div>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>