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Hi,<br><br>No, only for small values is should be off, maybe tau_t < 10 or 100 * delta_t.<br><br>How did you set up your harmonic oscillator?<br><br>Berk<br><br>> From: servaas.michielssens@student.kuleuven.be<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 7 May 2009 12:54:54 +0200<br>> Subject: [gmx-users] Re: v-rescale - harmonic oscillator<br>> <br>> Hi,<br>> <br>> Thank you for your reply.<br>> <br>> Yes by effective energy I mean the Gromacs conserved energy term.<br>> <br>> So you would say the cause of my problem here is that I need a small<br>> tau_t to thermostat this system but for small tau_t values the algorithm<br>> is not 100% ok yet? And what are very small tau_t values? I tested with<br>> quite a big range here.<br>> <br>> The problem occurred to me when I was experimenting with a hybrid monte<br>> carlo algorithm. I first tested it on a noble gas and compared to MD<br>> simulation with nose-hoover and v-rescale. Those results were 100%<br>> identical. Then I tried it on a dipeptide in vacuum, results were a<br>> little off here (I would expect this for nose-hoover thermostat, but not<br>> for v-rescale). So I decided to go the the extreme simple case of a<br>> harmonic oscillator. Those results were seriously off, and then I<br>> checked the conserved energy term, which seems impossible to keep it<br>> conserved for this system. (of course there can also be an error in my<br>> hybrid monte carlo code, but the fact that the conserved energy is not<br>> conserved is disturbing me here)<br>> <br>> <br>> Servaas<br>> <br>> <br>> <br>> <br>> Hi,<br>> <br>> What do you mean with effective energy?<br>> The Gromacs conserved energy term?<br>> <br>> For very small tau_t the current implementation does not work well.<br>> Bussi mailed me a proper implementation that I will put in when I have time.<br>> <br>> Berk<br>> <br>> > From: servaas.michielssens at student.kuleuven.be<br>> > To: gmx-users at gromacs.org<br>> > Date: Thu, 7 May 2009 09:02:52 +0200<br>> > Subject: [gmx-users] v-rescale - harmonic oscillator<br>> > <br>> > Hi,<br>> > <br>> > I did some experiments with a harmonic oscillator (diatomic molecule<br>> > without charge en LJ parameters) using the v-rescale thermostat. First I<br>> > ran a simulation in the NVE ensemble with a time-step of 0.0001ps, total<br>> > energy was constant here. <br>> > <br>> > Then I tried simulating the system with the v-rescale thermostat, same<br>> > time-step of 0.0001ps and tau_t=100,10,1,0.1,0.01,0.001. For none of<br>> > those simulations the effective energy was conserved. <br>> > (effective energy should be a conserved quantity for NVT simulations<br>> > with v-rescale thermostat, JOURNAL OF CHEMICAL PHYSICS Volume: 126<br>> > Issue: 1 Article Number: 014101 Published: JAN 7 2007 )<br>> > <br>> > So what is going wrong here? Would one expect this thermostat to fail<br>> > for such system (e.g. a simple Nose-Hoover is known to fail for the<br>> > harmonic oscillator)? <br>> > <br>> > <br>> > Thanks in advance,<br>> > <br>> > Servaas<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 /><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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