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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>That thermostat is really nice and also simple to implement.<br>It is now in CVS.<br><br>Thanks for the tip!<br><br>Berk.<br><br></div><br><hr id="stopSpelling">> 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 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 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>
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