Hi Berk, Thank you for your concern on this issue. It did not expect it to be a problem from the paper of Bussi et al., but it is of course possible. I am very curious to hear what they have to say about this. Are you contacting him or will I do it?
For the rotational degrees of freedom would removing them with comm_mode=angular be a problem then because you are using restraints? (you use orire than?) Thanks again, Servaas > Hi, > > With a diatomic molecule there is the issue that the rotation of the molecule > has two degrees of freedom > which are completely uncoupled from the rest of the system. > > Anyhow, I made a 1D harmonic oscillator using a position restraint and even > there the energy > does not seem to be conserved. > I am not sure if a harmonic oscillator is a pathetic case, like with > Nose-Hoover, > or if this is an issue with the integrator implementation in Gromacs. > I might need to ask Bussi about this. > > Berk > > > From: servaas.michielss...@student.kuleuven.be > > To: gmx-users@gromacs.org > > Date: Thu, 7 May 2009 14:03:30 +0200 > > Subject: [gmx-users] v-rescale - harmonic oscillator > > > > Hi, > > > > It is just a diatomic molecule without other interactions (so only > > bonded interaction, LJ=0 and charges=0 on the atoms). What other details > > would you like to know? Should I send you the tpr file? > > > > Servaas > > > > > > > > > > > > > > > Hi, > > > > > > No, only for small values is should be off, maybe tau_t < 10 or 100 * > > > delta_t. > > > > > > How did you set up your harmonic oscillator? > > > > > > Berk > > > > > > > From: servaas.michielss...@student.kuleuven.be > > > > To: gmx-users@gromacs.org > > > > Date: Thu, 7 May 2009 12:54:54 +0200 > > > > Subject: [gmx-users] Re: v-rescale - harmonic oscillator > > > > > > > > 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. 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