Hi Justin:
Thanks for your reply.
More spicifically, I still need to know how the value of friction
coefficient goes.
and also how PMFs of every pairs of ions goes. I am not actually asking how
to create PMF at this moment.
Thanks,
M. H. Rahman
----- Original Message -----
From: "Justin A. Lemkul" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: Friday, February 13, 2009 5:51 PM
Subject: Re: [gmx-users] Langevin Dyanamics in GROMACS
M Hafizur Rahman wrote:
Hi all:
Anyone can help me using Langevin Dynamics in GROMACS. Where does the
friction coefficient goes and How we can change the forece field to
include PMF.
For Langevin dynamics, read manual sections 3.8 or 3.9, depending on what
you want to do. Associated run control parameters are in section 7.3.3,
or online:
http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html
As for PMF, read manual sections 6.1, 6.3, and/or 6.4.
-Justin
Thanks,
M. Rahman
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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