From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Nov 12 2014 - 16:37:31 CST
Hi,
The Langevin thermostat and Langevin dynamics are really one in the
same, assuming you aren't talking about overdamped Langevin dynamics.
You can use generalized Born implicit solvent
(http://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node31.html) coupled
with "langevin on"
(http://www.ks.uiuc.edu/Research/namd/2.10b1/ug/node36.html).
I've used the "langevinFile" option to set different friction
coefficients for different particles. This means that you can set the
diffusion coefficient (in the long time limit) for your particles (or
molecules).
Best wishes,
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
On Wed, Nov 12, 2014 at 2:48 PM, Fidan Sumbul <fidansumbul_at_gmail.com> wrote:
> Dear NAMD users,
>
> I'd like to perform an implicit solvent Langevin Dynamics simulation. I can
> do it in Amber, but I wonder if I can use NAMD for this job because I am
> familiar with NAMD. Could you provide me a tutorial or link to a tutorial if
> NAMD does Langevin dynamics simulations. I know NAMD uses Langevin dynamics
> in normal MD simulations to keep temperature constant.
>
> Thanks for your help.
>
> --
> Fidan Sumbul
> PhD Student and T.A.
> Polymer Research Center
> Department of Chemical Engineering
> Bogazici University
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