<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Indeed, read the paper!<br><br>The stochastic term works on the "Berendsen scaling parameter" only.<br>It has the same correlation time as tau_t.<br>So the dynamics is nearly unaffected, surely less than with Nose-Hoover.<br></div><br>Berk.<br><br><hr id="stopSpelling">> Date: Thu, 24 Jul 2008 17:26:00 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Re: Question about Berendsen thermostat        and        Nose-Hoover temp coupling (chris.neale@utoronto.ca)<br>> <br>> Berk Hess wrote:<br>> > <br>> > Hi,<br>> > <br>> > That thermostat is really nice and also simple to implement.<br>> > It is now in CVS.<br>> If this thermostat has a stochastic term, is the dynamics still <br>> meaningful then?<br>> <br>> (I haven't read the paper of course :)).<br>> > <br>> > Thanks for the tip!<br>> > <br>> > Berk.<br>> > <br>> > <br>> > > Date: Wed, 23 Jul 2008 10:12:36 -0400<br>> > > From: michael.shirts@columbia.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: [gmx-users] Re: Question about Berendsen thermostat and <br>> > Nose-Hoover temp coupling (chris.neale@utoronto.ca)<br>> > ><br>> > > Note that a recently a velocity rescaling algorithm was developed in<br>> > > the Parrinello group that does give the correct canonical ensemble.<br>> > > See: http://arxiv.org/abs/0803.4060. It might be nice to replace<br>> > > Berendsen with this algorithm, which should have the nice properties<br>> > > of Berendsen (converges to the constraint temperature quickly) without<br>> > > the serious drawbacks.<br>> > ><br>> > > Cheers,<br>> > > Michael<br>> > ><br>> > > On Wed, Jul 23, 2008 at 10:10 AM, Michael Shirts<br>> > > <michael.shirts@columbia.edu> wrote:<br>> > > >> Have you seen any information to suggest that this is actually a<br>> > > >> non-trivial concern? That is, given static point charges, an empirical<br>> > > >> LJ force, short cutoffs, etc., do you believe that the application of<br>> > > >> nose-hoover, berendsen, or even the arbitrary velocity rescaling<br>> > > >> significantly degrades the quality of the obtained dynamics?<br>> > > ><br>> > > > 1) I think there's an important distinction to be made here between<br>> > > > accuracy and physical validity. If you use a thermostat, then the<br>> > > > dynamic properties you obtain for the system will be different than<br>> > > > the properties obtained without the thermostat, independent of what<br>> > > > model you choose. So, I don't know that it's that useful to ask<br>> > > > whether the differences from the true system due to thermostat are<br>> > > > large compared to the differences due to the choice of model -- the<br>> > > > results are going to be dependent on the thermostat, so the field has<br>> > > > chosen a standard definition of the dynamics, one that most resembles<br>> > > > the actual physical system (where there isn't temperature rescaling<br>> > > > every 2 fs or a piston coupled to a 10 nm cube of water, etc).<br>> > > ><br>> > > > 2) If one uses the Berendsen thermostat, then statistical mechanics of<br>> > > > canonical ensembles will not strictly apply, and one can't use many of<br>> > > > the results one would like to (or, are using already incorrectly).<br>> > > > One can do physics-based simulation of molecular models, or one can do<br>> > > > non-physics-based simulations of molecular models. In many cases, the<br>> > > > non-physics-based results will be statistically indistinguishable from<br>> > > > the physics based results. But why bother with an uncontrolled<br>> > > > approximation when you don't -have- to use one? It just adds another<br>> > > > chance that what one simulates is not reproducible or reliable, and<br>> > > > heaven knows that simulation currently has enough of those already.<br>> > > ><br>> > > > It's like building a tower out of blocks, and each uncontrolled<br>> > > > approximation, no matter how small, is a bit of unevenness in the<br>> > > > block. If you have just one wobbly block, you can stand on it pretty<br>> > > > well -- you know the limits of the approximation, you can get a pretty<br>> > > > good sense of what's going on with the system. Once there's a large<br>> > > > number of wobbly blocks, though -- good luck standing on top of it and<br>> > > > trying to build good science. As simulations get larger and more<br>> > > > complicated, they are built out of more and more blocks, and we need<br>> > > > to make sure we're paying careful attention to how well they all fit<br>> > > > together.<br>> > > ><br>> > > > Best,<br>> > > > Michael Shirts<br>> > > > Research Fellow<br>> > > > Columbia University<br>> > > > Department of Chemistry<br>> > > ><br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > Express yourself instantly with MSN Messenger! MSN Messenger <br>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone:        +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se        spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>