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Hi,<br><br>I have come to the conclusion that the v-rescale thermostat is only correct<br>in the limit of large numbers of degrees of freedom, which is equivalent to a small scaling limit.<br>The conservation of the conserved energy quantity improves as the system gets bigger.<br><br>But I noticed that in 4.0 the energy conservation is not good.<br>It can be improved significantly by changing line 164 or src/mdlib/update.c from<br>vv = lg*(vn + f[n][d]*w_dt);<br>to<br>vv = lg*vn + f[n][d]*w_dt;<br><br>There are some other similar lines in case you are PR p-coupling or cosine acceleration.<br><br>I will probably not fix this for 4.0.5, but only for 4.1, so we do not change<br>the reproducibility in minor revisions.<br><br>Berk<br><br><br>> From: servaas.michielssens@student.kuleuven.be<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 7 May 2009 15:27:37 +0200<br>> Subject: [gmx-users] Re: v-rescale - harmonic oscillator<br>> <br>> Hi Berk,<br>> <br>> Thank you for your concern on this issue. It did not expect it to be a<br>> problem from the paper of Bussi et al., but it is of course possible. <br>> I am very curious to hear what they have to say about this. Are you<br>> contacting him or will I do it?<br>> <br>> For the rotational degrees of freedom would removing them with<br>> comm_mode=angular be a problem then because you are using restraints?<br>> (you use orire than?)<br>> <br>> Thanks again,<br>> <br>> Servaas<br>> <br>> > Hi,<br>> > <br>> > With a diatomic molecule there is the issue that the rotation of the molecule has two degrees of freedom<br>> > which are completely uncoupled from the rest of the system.<br>> > <br>> > Anyhow, I made a 1D harmonic oscillator using a position restraint and even there the energy<br>> > does not seem to be conserved.<br>> > I am not sure if a harmonic oscillator is a pathetic case, like with Nose-Hoover,<br>> > or if this is an issue with the integrator implementation in Gromacs.<br>> > I might need to ask Bussi about this.<br>> > <br>> > Berk<br>> > <br>> > > From: servaas.michielssens@student.kuleuven.be<br>> > > To: gmx-users@gromacs.org<br>> > > Date: Thu, 7 May 2009 14:03:30 +0200<br>> > > Subject: [gmx-users] v-rescale - harmonic oscillator<br>> > > <br>> > > Hi,<br>> > > <br>> > > It is just a diatomic molecule without other interactions (so only<br>> > > bonded interaction, LJ=0 and charges=0 on the atoms). What other details<br>> > > would you like to know? Should I send you the tpr file?<br>> > > <br>> > > Servaas<br>> > > <br>> > > <br>> > > <br>> > > > <br>> > > > <br>> > > > 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>> <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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