Re: langevinDamping

From: Hyundeok Song (songhk_at_email.uc.edu)
Date: Sun Nov 16 2008 - 18:03:58 CST

I red one paper that explains how to choose the frictional coefficient numerically -TABLE I
(Computing memory functions from molecular dynamics simulations, G.R. Kneller and K. Hinsen,
Journal of chemical physics, Volume 115, number 24, 22 December 2001, 11097-11105)
 And they compared it with the frictional coefficient computed from the diffusion constant.
( k_B * T / m * D).

So, I think we can choose the frictional coefficient from the diffusion constant. And Dr. Jérôme Hénin answered similar question at NAMD.

 Jérôme Hénin
" For the biological systems I've simulated, values around 1 ps-1 were good trade-offs. You should only need more if strongly exothermal phenomena happen in your system - maybe when starting the equilibration of a new system - but
then usually you don't mind too much if temperature raises a little for a short time. "
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0620.html

If someone add more exact answer(comment), I will be glad.

hyun.

---- Original message ----
>Date: Fri, 14 Nov 2008 21:45:10 -0500
>From: "Roman Petrenko" <rpetrenko_at_gmail.com>
>Subject: namd-l: langevinDamping
>To: namd-l_at_ks.uiuc.edu
>
>Dear all,
>how to choose damping coefficient for Langevin dynamics.
>In three articles which used NAMD i found the following values 1, 5
>and 10 ps-1. Is there any guidance how to choose it? I am simulating
>peptides 20-30 residues long in water box with PBC with langevin
>barostat and thermostat.
>
>--
>Roman Petrenko.
>Physics Department
>University of Cincinnati
>

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