[gmx-users] Re: v-rescale - harmonic oscillator

servaas servaas.michielssens at student.kuleuven.be
Thu May 7 12:54:54 CEST 2009


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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