Dear Gromacs Users,
I have doubt about temperature bath coupling (v-rescale). I use this method
(v-rescale) for my system, and my system is NPT ensemble.
Has it problem? is v-rescale just used for NVT ensemble or it doesn't have
restriction?
Please help me.
Thank you in advance
Best Regards
Hi Sara,
NPT also requires a routine for temperature coupling. What makes you wonder
about the suitability of v-rescale for that? If you check the mdp files
from tutorial stuff, you'll probably encounter the v-rescale method used in
the NpT simulations.
Cheers,
Tsjerk
On Sep 18, 2012 7:12 AM,
Dear users,
what is the literature reference for using the V-Rescale Thermostat? Maybe the
Gromacs 4 paper?
Thank you
---
Ricardo O. S. Soares , PhD Student.
Group of Biological Physics - Department of Physics Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of
There's a reference in the gromacs manual
Ricardo O. S. Soares skrev 2011-03-03 22.52:
Dear users,
what is the literature reference for using the V-Rescale Thermostat?
Maybe the Gromacs 4 paper?
Thank you
---
Ricardo O. S. Soares , PhD Student.
Group of Biological Physics -
Ok, thanks Erik.
De: Erik Marklund er...@xray.bmc.uu.se
Para: Discussion list for GROMACS users gmx-users@gromacs.org
Cc: Ricardo O. S. Soares ross_...@yahoo.com.br
Enviadas: Quinta-feira, 3 de Março de 2011 18:58:30
Assunto: Re: [gmx-users] V-Rescale
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
I want to keep the T at 300K, so does it matter to select any thermostat method?
Another note when i use PME:
gromacs wrote:
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale thermostat.
I want to keep the T at 300K, so does it matter to select any thermostat
method?
The
On 26/01/2011 12:05 AM, Justin A. Lemkul wrote:
gromacs wrote:
HI Friends,
I get the following note,
The Berendsen thermostat does not generate the correct kinetic energy
distribution. You might want to consider using the V-rescale
thermostat.
I want to keep the T at 300K, so does it
= 300
gen_seed = 1993
Message: 4
Date: Tue, 25 Jan 2011 08:05:44 -0500
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] V-rescale thermostat, PME, Estimate for the
relativecomputational load of the PME mesh part
Dear gromacs users,
I am running NVT simulations for polarizable (shell particle) water model
(GROMACS version 4.5.1 and 4.5.3 (issue is same in both)) using v-rescale
thermostat.
While temperature, potential, kinetic and total energies behave quite well I am
failing to obtain constant values
to the surface tension
analytically.
Berk
From: mstu...@slb.com
To: gmx-users@gromacs.org
Date: Wed, 1 Dec 2010 12:10:23 +
Subject: [gmx-users] v-rescale and conserved energy
Dear gromacs users, I am running NVT simulations for polarizable (shell
particle) water model (GROMACS version 4.5.1
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
@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
the current implementation does not work well.
Bussi mailed me a proper implementation that I will put in when I have time.
Berk
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
:03:30 +0200
Subject: [gmx-users] v-rescale - harmonic oscillator
Hi,
It is just a diatomic molecule without other interactions (so only
bonded interaction, LJ=0 and charges=0 on the atoms). What other details
would you like to know? Should I send you the tpr file?
Servaas
Hi
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