[gmx-users] langevin dynamics
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Tue Aug 1 10:59:42 CEST 2006
On 7/31/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
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> 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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