Dear Servaas,
the problem that you found is not related to the stochastic rescaling
itself, but to the way the effective energy is calculated in gromacs.
In particular, the increment in the integral part is not consistent
with the applied scaling. You can correct for this by changing
am prepared to help with it or test
it if this is required.
Kind regards,
Servaas
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Message: 1
Date: Tue, 12 May 2009 09:06:52 +0200
From: Giovanni Bussi giovanni.bu...@gmail.com
Subject: [gmx-users] Re: v-rescale - harmonic oscillator
To: gmx-users@gromacs.org
...@student.kuleuven.be
To: gmx-users@gromacs.org
Date: Tue, 12 May 2009 13:25:02 +0200
Subject: [gmx-users] Re: v-rescale - harmonic oscillator
Dear Dr. Bussi,
Thank you very much for the explanation of this problem.
So I understand that a problem remains with the integrator used
will probably not fix this for 4.0.5, but only for 4.1, so we do not change
the reproducibility in minor revisions.
Berk
From: servaas.michielss...@student.kuleuven.be
To: gmx-users@gromacs.org
Date: Thu, 7 May 2009 15:27:37 +0200
Subject: [gmx-users] Re: v-rescale - harmonic oscillator
Hi Berk
: Berk Hess g...@hotmail.com
Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: col113-w10f68330ea113929cbc3518e...@phx.gbl
Content-Type: text/plain; charset=iso-8859-1
Hi,
I have come to the conclusion
@gromacs.org
Date: Fri, 8 May 2009 11:17:33 +0200
Subject: [gmx-users] Re: v-rescale - harmonic oscillator
Hi,
Thanks for your confirmation of this problem. One thing is not clear to
me from your answer. Has v-rescale fundamental problems with a Harmonic
oscillator or is it a problem
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?
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
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