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, [EMAIL PROTECTED] <[EMAIL PROTECTED]>
wrote:
Send gmx-users mailing list submissions to
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?
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
--
Edgar Luttmann, PhD
Stanford University, Stanford, CA, USA
Department of Chemistry, Group of Prof. Dr. V. Pande
postdoctoral researcher: [EMAIL PROTECTED] - distributed computing
Clark Center, 94305-5080 Stanford, CA, phone: (650) 723 1097
email: luttmann AT stanford.edu, www: http://www.stanford.edu/~luttmann
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
