[gmx-users] Re: v-rescale - harmonic oscillator
gmx3 at hotmail.com
Thu May 7 13:48:53 CEST 2009
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?
> From: servaas.michielssens at student.kuleuven.be
> To: gmx-users at gromacs.org
> Date: Thu, 7 May 2009 12:54:54 +0200
> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
> 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)
> 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.
> > 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
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