**From:** Jeff Comer (*jeffcomer_at_gmail.com*)

**Date:** Thu Nov 13 2014 - 14:37:13 CST

**Next message:**Jeff Comer: "Re: Can NAMD does Langevin Dynamics Simulation"**Previous message:**Kenno Vanommeslaeghe: "Re: namd simulation for solids withoy solvation"**In reply to:**Fidan Sumbul: "Re: Can NAMD does Langevin Dynamics Simulation"**Next in thread:**Jeff Comer: "Re: Can NAMD does Langevin Dynamics Simulation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear Ms Sumbul,

The difference between a Langevin thermostat and Langevin dynamics is

the strength of the coupling. The algorithm is identical. When used as

a thermostat in an explicit solvent simulation, the damping constant

is typically small and only slightly perturbs the dynamics, although

it includes both dissipation and a random force.

Let's say you have a simulation of a single Na+ ion with explicit

water molecules and no thermostat — just Newton's second law. If you

look at the motion on a long enough timescale (roughly >1 ps), you'll

see the Na+ ion acts like it is Brownian particle with a diffusion

coefficient of D=133 Å^2/ns (assuming your force field agrees with

experiment). This is how diffusive motion emerges in real life —

although the underlying motion is Newtonian, the Na+ ion bounces off a

bunch of chaotically moving water molecules and diffusive motion

naturally emerges.

Let's calculate what langevinDamping coefficient this diffusive motion

would correspond to. langevinDamping = kT/(mD), where kT is the

thermal energy, m is the mass, and D is the diffusion coefficient.

NAMD takes langevinDamping in units of ps^-1. Using the program GNU

units, I calculate

units 'k (300K)/(22.9898u 133*angstroms^2/ns)' 'ps^-1'

81.577159

This damping coefficient is much much bigger than people typically use

as a thermostat (~1 ps^-1). Hence, in an explicit water simulation,

the natural dissipation and random buffeting is 80 times more than is

typically used for maintaining the temperature. A 1 ps^-1 damping

constant has little effect on the dynamics of the ion, but applied to

the whole system, is sufficient to maintain the temperature. On the

other hand, a 20 ps^-1 damping constant on the whole system will

measurably reduce the diffusion coefficient of the ion. I've done this

for water in:

http://dx.doi.org/10.1021/ct300867e

Getting back to the implicit solvent simulations, what we just

calculated is the langevinDamping coefficient we'd need to emulate the

effect of explicit water molecules on the ion. I just ran NAMD for 200

ps for a system consisting of a single Na+ ion. Here are the

thermostat parameters I used:

langevin on

langevinTemp 300

langevinHydrogen on

langevinDamping 81.577159

*>From the trajectory, I estimated the diffusion coefficient by
*

<Δx^2>/(2Δt) and that gives 136.266 Å^2/ns, which is pretty close to

the diffusion coefficient that we wanted. So to run Langevin dynamics

on an implicit solvent model in NAMD, you set langevinDamping to

kT/(mD). If you have atoms or particles with different diffusion

coefficients, you can use langevinFile to set the damping constants

individually.

I hope this is clear!

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 Thu, Nov 13, 2014 at 10:41 AM, Fidan Sumbul <fidansumbul_at_gmail.com> wrote:

*> 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?
*

*>
*

*> Regards,
*

*>
*

*>
*

*> On Thu, Nov 13, 2014 at 12:37 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
*

*>>
*

*>> 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
*

*>
*

*>
*

*>
*

*>
*

*> --
*

*> Fidan Sumbul
*

*> PhD Student and T.A.
*

*> Polymer Research Center
*

*> Department of Chemical Engineering
*

*> Bogazici University
*

**Next message:**Jeff Comer: "Re: Can NAMD does Langevin Dynamics Simulation"**Previous message:**Kenno Vanommeslaeghe: "Re: namd simulation for solids withoy solvation"**In reply to:**Fidan Sumbul: "Re: Can NAMD does Langevin Dynamics Simulation"**Next in thread:**Jeff Comer: "Re: Can NAMD does Langevin Dynamics Simulation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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