Le 08/05/13 19:33, Christoph Junghans a écrit :
Date: Wed, 08 May 2013 16:34:46 +0200
From: Julian Garrec
Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS
vs AMBER
To: Discussion list for GROMACS users
Message-ID: <518a6286.8020...@epfl.ch>
Content-Type
quantities such as
the friction coeficient in equation 3.114 of the manual (v4.6.1).
Please help,
Sincerely,
Julian
Le 04/05/13 13:42, Julian Garrec a écrit :
Dear all,
I am trying to use stochastic dynamics in GROMACS to reproduce some
previous results that I got with the AMBER software
he same spirit).
3) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ?
Thanks for your help,
Julian
--
Julian Garrec, research associate
Web: https://sites.google.com/site/juliangarrec/
Équipe : Chimie et Biochimie Théoriques
Unité Mixte de Recherches CNRS UHP 756
Thank you very much for your clear reply.
Best regards,
Julian Garrec
Le 25/05/12 17:17, Mark Abraham a écrit :
On 25/05/2012 7:44 PM, Julian Mondon-Garrec wrote:
Hi all,
I am trying to get the electrostatic forces acting on each atom as a
function of time. I have checked the list and all
and vdw components from the forces ? One option could be to set
all the unwanted interaction to zero in the topology file but I am
wondering if there is a safer alternative.
Cheers,
--
Julian Garrec, post-doc
Tel: ++41 (0)21 69 303 27
Web: https://sites.google.com/site/juliangarrec
ame as the second half (with the proper shifting) of
the output of
g_msd -b 0 -e 100 -trestart 50
But it is not, as anyone can verify with any simulation.
.. what are we missing?
Thanks in advance,
Julian
--
Julian Gelman Constantin
Department of Inorganic, Analytic and Chemical Physi
Justin A. Lemkul wrote:
Julian Garrec wrote:
Justin A. Lemkul wrote:
Julian Garrec wrote:
Dear GROMACS users,
I am trying to equilibrate my system (monomeric protein in water) and
I want to use position restraint on heavy atoms of the solute using
the posre.itp file. For
Justin A. Lemkul wrote:
Julian Garrec wrote:
Dear GROMACS users,
I am trying to equilibrate my system (monomeric protein in water) and I
want to use position restraint on heavy atoms of the solute using the
posre.itp file. For some reason, grompp applies correctly the force
constant I
00e+00, 0.e+00), fcB=(
5.6700e+02, 5.6700e+02, 5.6700e+02)
Using the -debug option with grompp didn't provide me further information.
Does anybody know how to cure this problem ?
Thanks,
Julian
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