Hi, Thank you for your reply.
Yes by effective energy I mean the Gromacs conserved energy term. So you would say the cause of my problem here is that I need a small tau_t to thermostat this system but for small tau_t values the algorithm is not 100% ok yet? And what are very small tau_t values? I tested with quite a big range here. The problem occurred to me when I was experimenting with a hybrid monte carlo algorithm. I first tested it on a noble gas and compared to MD simulation with nose-hoover and v-rescale. Those results were 100% identical. Then I tried it on a dipeptide in vacuum, results were a little off here (I would expect this for nose-hoover thermostat, but not for v-rescale). So I decided to go the the extreme simple case of a harmonic oscillator. Those results were seriously off, and then I checked the conserved energy term, which seems impossible to keep it conserved for this system. (of course there can also be an error in my hybrid monte carlo code, but the fact that the conserved energy is not conserved is disturbing me here) Servaas Hi, What do you mean with effective energy? The Gromacs conserved energy term? For very small tau_t the current implementation does not work well. Bussi mailed me a proper implementation that I will put in when I have time. Berk > From: servaas.michielssens at student.kuleuven.be > To: gmx-users at gromacs.org > Date: Thu, 7 May 2009 09:02:52 +0200 > Subject: [gmx-users] v-rescale - harmonic oscillator > > Hi, > > I did some experiments with a harmonic oscillator (diatomic molecule > without charge en LJ parameters) using the v-rescale thermostat. First I > ran a simulation in the NVE ensemble with a time-step of 0.0001ps, total > energy was constant here. > > Then I tried simulating the system with the v-rescale thermostat, same > time-step of 0.0001ps and tau_t=100,10,1,0.1,0.01,0.001. For none of > those simulations the effective energy was conserved. > (effective energy should be a conserved quantity for NVT simulations > with v-rescale thermostat, JOURNAL OF CHEMICAL PHYSICS Volume: 126 > Issue: 1 Article Number: 014101 Published: JAN 7 2007 ) > > So what is going wrong here? Would one expect this thermostat to fail > for such system (e.g. a simple Nose-Hoover is known to fail for the > harmonic oscillator)? > > > Thanks in advance, > > Servaas > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
