From: Fidan Sumbul (fidansumbul_at_gmail.com)
Date: Thu Nov 13 2014 - 10:41:39 CST
Thank you for your response Dr. Comer.
I'd like to perform Langevin dynamics simulation (stochastic dynamis), but
not overdamped as Brownian dynamics.
If Langevin thermostat and Langevin dynamics are the same, why we call
Molecular dynamics that NAMD MD runs do with langevin thermostat?
Could you please help me to understand what is the real distinction between
MD simulations with Langevin thermostat and Langevin dynamics simulations?
Does MD with Langevin thermostat also have random force?
On Thu, Nov 13, 2014 at 12:37 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> 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"
> 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
> Best wishes,
> 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>
> > Dear NAMD users,
> > I'd like to perform an implicit solvent Langevin Dynamics simulation. I
> > 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
> > 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
-- Fidan Sumbul PhD Student and T.A. Polymer Research Center Department of Chemical Engineering Bogazici University
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