Maria,<br>
<br>
I remember looking into this on the list at one point, too, and I
concluded that as far as I can tell, Parrinello-Rahman probably doesn't
work properly at present. I seem to recall seeing a bunch of discussion
of this on the developers list, and I found this message from Michael
Shirts particularly concerning:
<a href="http://www.gromacs.org/pipermail/gmx-developers/2004-May/000877.html">http://www.gromacs.org/pipermail/gmx-developers/2004-May/000877.html</a>.
So I concluded I should avoid Parrinello-Rahman.<br>
<br>
The problem with Nose-Hoover is that with the leapfrog integration
method that GROMACS currently uses, it's not reversible. I'm not sure
this is necessarily that big of a problem; it depends on what you want
to do. If you are doing something which requires reversibility
obviously this is a problem. There are other problems with Nose-Hoover,
of course, as in this message you point to
(<a href="http://www.gromacs.org/pipermail/gmx-users/2004-November/013017.html">http://www.gromacs.org/pipermail/gmx-users/2004-November/013017.html</a>)
-- but those aren't problems with the GROMACS version of Nose-Hoover,
but with Nose-Hoover generally. See especially the Toda demon paper --
it's particularly informative, and probably you can get an idea from
there some checks you could do to see whether it is working "OK" for
the system you're using.<br>
<br>
I've had some experience where it works OK, but it also (as you might
expect) seems to work particularly poorly when you are applying it to
anything with a relatively small number of degrees of freedom. I've
finally ended up using Langevin (stochastic) dynamics for my
calculations as a "thermostat" because I needed something that could
cope with decoupling calculations (turning off interactions between a
ligand and a protein) without giving crazy results. I don't really
trust either Berendsen or Nose-Hoover in that case, and the Anderson
thermostat isn't quite implemented yet.<br>
<br>
Someone else may be able to comment in nore detail on the
Rahman-Parrinello issue. I only know what I read on the list, which
seemed concerning.<br>
<br>
David Mobley<br>
<br><br><div><span class="gmail_quote">On 1/1/06, <b class="gmail_sendername">maria papadopoulou</b> <<a href="mailto:maria_papadopoulou55@hotmail.com">maria_papadopoulou55@hotmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi<br><br>As someone interested in using gromacs I have been looking at the mailing<br>list and trying to decide on which temp and presure coupling method to use.<br>My preference would be to use Nose Hoover for temp and Parrinello Rahman
<br>for pressure coupling, but I have read some posts that suggest that there<br>are problems with these methods in gromacs:<br><br>NH<br><a href="http://www.gromacs.org/pipermail/gmx-developers/2005-March/001062.html">http://www.gromacs.org/pipermail/gmx-developers/2005-March/001062.html
</a><br><a href="http://www.gromacs.org/pipermail/gmx-users/2004-November/013017.html">http://www.gromacs.org/pipermail/gmx-users/2004-November/013017.html</a><br>Parrinello Rahman<br><a href="http://www.gromacs.org/pipermail/gmx-users/2003-October/007426.html">
http://www.gromacs.org/pipermail/gmx-users/2003-October/007426.html</a><br><a href="http://www.gromacs.org/pipermail/gmx-users/2003-October/007426.html">http://www.gromacs.org/pipermail/gmx-users/2003-October/007426.html</a>
<br>and in paticular the fix mentione in the following link, for which i can<br>find no further detials of:<br><a href="http://www.gromacs.org/pipermail/gmx-users/2004-January/008670.html">http://www.gromacs.org/pipermail/gmx-users/2004-January/008670.html
</a><br><br>Could someone please advise me as to how serious these problems are in<br>paricular when using parrinello rahman with an octahedral box and isotropic<br>pressure coupling.<br><br>I have v 3.2.1 installed<br><br>
Thanks<br><br>Maria<br><br>_________________________________________________________________<br>Be the first to hear what's new at MSN - sign up to our free newsletters!<br><a href="http://www.msn.co.uk/newsletters">http://www.msn.co.uk/newsletters
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