**From:** Blake Charlebois (*bdc_at_mie.utoronto.ca*)

**Date:** Fri Jul 15 2005 - 00:05:03 CDT

**Next message:**Hidekazu WATANABE: "patch failed"**Previous message:**Stern, Julie: "patch PYRT and extending DNA"**Next in thread:**\: "Re: Random forces in Langevin temperature control -- three questions"**Reply:**\: "Re: Random forces in Langevin temperature control -- three questions"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello everyone,

I would like to better understand the random force R applied in Langevin

temperature control.

BACKGROUND:

According to Tobias, Martyna, and Klein (J. Phys. Chem. 97(49):12959, 1993),

the governing equation (I will change variable names and use [...] for

subscripts) in, I assume, one dimension is

m[i]*a[i] = F[i] - m[i]*gamma[i]*v[i] + R[i](t)

and

"...R(t) is a Gaussian stochastic variable with zero mean and variance..."

<R[i](t)*R[i](t')> = 2*m[i]*gamma[i]*kB*T*delta(t-t')

Schneider and Stoll (Phys. Rev. B 17(3):1302, 1978) also give a description.

Here are my questions:

QUESTION ONE:

Variables t, t', and i appear on both sides of <R[i](t)*R[i](t')> =

2*m[i]*gamma[i]*kB*T*delta(t-t'). What type of averaging is <...> supposed

to represent here? Schneider and Stoll use <R[i](t)*R[k](t+tau)> =

2*m[i]*gamma[i]*kB*T*Kronecker_delta[i,k]*Dirac_delta(tau). Does this mean

that <...> denotes averaging over t, and that Tobias et al. have used

slightly confusing notation, or am I missing something?

QUESTION TWO:

It seems to me that the dimensions of the left- and right-hand sides of

<R(t)*R(t')> = 2*m*gamma*kB*T*delta(t-t') do not agree. What blunder am I

making here?

The dimensions of gamma are (time)^(-1).

The dimensions of 2*m*gamma*kB*T*delta(t-t') are

(mass)*(time)^(-1)*(force)*(distance) or (force)^2*(time).

The dimensions of <R(t)*R(t')> are (force)^2.

QUESTION THREE:

If delta(t-t') is the Dirac delta function, then the mean squared force is

infinity when t=t'. Schneider and Stoll, through mathematics I do not fully

understand at the moment, write R (they call it eta) in terms of random

variables and delta functions, allowing the elimination of the delta

functions when the equations of motion are integrated (I think). I have also

looked briefly at the NAMD 2.5 source code (file Sequencer.C, lines 278-286,

451-514; file Molecule.C, lines 3969-4160), but I do not fully understand it

either. In practice, what is the mean squared random force in a given

direction?

Any help with one or more of these questions would be much appreciated.

Blake Charlebois

**Next message:**Hidekazu WATANABE: "patch failed"**Previous message:**Stern, Julie: "patch PYRT and extending DNA"**Next in thread:**\: "Re: Random forces in Langevin temperature control -- three questions"**Reply:**\: "Re: Random forces in Langevin temperature control -- three questions"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 05:18:53 CST
*