[gmx-users] v-rescale - harmonic oscillator

Berk Hess gmx3 at hotmail.com
Thu May 7 12:24:00 CEST 2009


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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