[gmx-users] langevin dynamics
luttmann at stanford.edu
Tue Aug 1 11:57:52 CEST 2006
The bd_fric=0 results in the usage of mass/tau_t as the friction
coefficient. You should find the tau_t option somewhere in the output as
As David mentioned, changing tau_t changes the results. And this leads
me to one question, as I see an increase in average temperature upon
decreasing the tau_t.
@David: As you used different friction coefficients I would be curious
if you can observe the same dependency?
pim schravendijk wrote:
> On 7/31/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
>> Send gmx-users mailing list submissions to
>> Date: Mon, 31 Jul 2006 07:21:46 -0700
>> From: "David Mobley" <dmobley at gmail.com>
>> Subject: Re: [gmx-users] langevin dynamics
>> Gerrit is right, with "sd", the friction is set by tau_t, as described
>> in the section on SD in the manual. In my hands, different tau_t with
>> sd does make a significant difference in what goes on...
>> On 7/31/06, Gerrit Groenhof (RUG) <g.groenhof at rug.nl> wrote:
>> > I think you do not use the bd_fric in combination with sd, but with bd,
>> > the friction is set by the tau_t instead. Did you als use different
>> > parameters for that?
>> > For bd, you would use the friction bd_fric to set the ld friction, but
>> > not for sd, but I could be wrong here...
> I know this is correctly mentioned in the manual, but if you look at the
> mdout.mdp file, it says:
> ; LANGEVIN DYNAMICS OPTIONS
> ; Friction coefficient (amu/ps) and random seed
> bd-fric = 0
> ld-seed = 1993
> which just makes things more confusing than they already are. Maybe a
> suggestion to more clearly indicate the bd and sd parameters in there?
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Edgar Luttmann, PhD
Stanford University, Stanford, CA, USA
Department of Chemistry, Group of Prof. Dr. V. Pande
postdoctoral researcher: Folding at home - distributed computing
Clark Center, 94305-5080 Stanford, CA, phone: (650) 723 1097
email: luttmann AT stanford.edu, www: http://www.stanford.edu/~luttmann
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