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
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 f
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 s
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 Sand
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 ca
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
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
ru
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 ce
lss...@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 probl
is. I 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
> Subject: [gmx-users] Re: v-rescale - harmonic oscillator
> To: gmx-user
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
src/mdlib/cou
o: gmx-users@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 Harmo
> From: Berk Hess
> Subject: RE: [gmx-users] Re: v-rescale - harmonic oscillator
> To: Discussion list for GROMACS users
> Message-ID:
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
>
> I have come to the conclusion that the v-rescale ther
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 oscill
vaas
> >
> >
> >
> > >
> > >
> > > 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?
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]
Hi,
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?
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