Peter C. Lai wrote
Generally it's probably not a good idea to rely on tutorials designed
around 3.3 when a google search for gromacs tutorial shows a series of
4.5.x
tutorials written by Justin himself, with explanations of why certain
steps
are conducted. (also when certain features may
Hi Peter,
Thanks for your response.
Rather than dragging this thread too far off-topic, I'll direct you back to
my thread, where I have just posted additional details. I took a warning
message from GROMACS a bit too literally and it caused me to use conditions
that blew up my simulations.
I am
On 2012-09-20 12:18:02AM -0700, Ladasky wrote:
Hi Peter,
Thanks for your response.
Rather than dragging this thread too far off-topic, I'll direct you back to
my thread, where I have just posted additional details. I took a warning
message from GROMACS a bit too literally and it caused
On 20/09/12 01:35, Peter C. Lai wrote:
then switching to nose-hoover for production
runs (as nose-hoover chains result in the correct canonical distribution)?
I was under the impression that v-rescale resulted in the correct
canonical distribution as well. Is this incorrect?
--
Massimo
On 20/09/2012 9:35 AM, Peter C. Lai wrote:
I am not sure where the idea of using berendsen barostat with the v-rescale
thermostat for equilibration came from, however. Doesn't the typical
equilibration begin with v-rescale for temperature equilibration then
adding parinello-rahman barostat then
I've done some extensive testing (paper on testing method in the
works) and vrescale gives a very accurate ensemble very well for NVT.
Parrinello-Rahman and MTTK are the only algorithms that are correct
for NPT. Berendsen barostat is not. Note that there is a bug with
vrescale + md-vv + that is
Dear Sara,
I just had a problem with my simulations that I traced to the use of the
V-rescale temperature algorithm. Here is my recent post:
http://gromacs.5086.n6.nabble.com/Re-Water-molecules-cannot-be-settled-why-td4999302.html;cid=1348087067061-71#a5001121
V-rescale may be appropriate in
I am not sure where the idea of using berendsen barostat with the v-rescale
thermostat for equilibration came from, however. Doesn't the typical
equilibration begin with v-rescale for temperature equilibration then
adding parinello-rahman barostat then switching to nose-hoover for production
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
-
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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