[gmx-users] langevin dynamics

[Edgar Luttmann]

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 
well.

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?

Cheers,
Edgar


pim schravendijk wrote:
> On 7/31/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
> wrote:
>>
>> 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...
>>
>> David
>>
>>
>> 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