On 7/31/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:
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Date: Mon, 31 Jul 2006 07:21:46 -0700
From: "David Mobley" <[EMAIL PROTECTED]>
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) < [EMAIL PROTECTED]> 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?
--
greetings, Pim
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