**From:** *gamini_at_ncbs.res.in*

**Date:** Tue Jul 11 2006 - 15:36:45 CDT

**Next message:**Pijush Ghosh: "RE: force calculation during to conformational change"**Previous message:**Gaurav Sharma: "force calculation during to conformational change"**Next in thread:**Peter Freddolino: "Re: Computing Potential of Mean Force --SMD-cv"**Reply:**Peter Freddolino: "Re: Computing Potential of Mean Force --SMD-cv"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear Namd users,

Hi !!

I would like to understand on how to computationally evaluate the

potential of mean force for a given non-equlibrium process using SMD-cv

approach.

To start with, I have considered the process of unfolding of ubiquitin.

Ubiquitin unfolding was simulated using Steered Molecular Dynamics

-constant velocity pulling, as illustrated in the tutorial.

I have the following data(output) in log file:

The positions of the SMD atom, x y z

*>From this, I have computed, the extension as center-center distance
*

euclidean)between the fixed(x,y,z) and SMD(x,y,z)atom.

Therefore, I have the timeseries for extension.

Also given in the log file are the three components of forces( fx,fy,fz).

I have calculated force as (nx*fx+ny*fy+nz*fz), where nx,ny,nz are

normalized vetors.

Now, I have the timeseries for force.

I have the following questions regarding the same.

a)I would like to understand, given the available output from such

simulation (SMD-cv), how to reconstruct the potential of mean force

computationally?

b)From what limited understanding I have from the literature

(Reference: Jensen et al;PNAS (2002), vol 99,6731-6736 ),

the potential of mean force can be computed from Jarzynski's identity by

cumulant expansion(to second order for accuracy)as :

<W(t)> - 1/2KbT{[<W(t)^2>] -[<W(t)>^2] }

Is it correct that I evaluate the above expression for computing potential

of mean force ?

c)And, Is W(t) evaluated as:

W(t)= {/ 0 to t(v*f(t)*dt)} - k/2[R(t)- R0 -v*t]^2

where,

/ 0 to t =integral 0 to t (sorry!! I had to limit my use of symbols)

R(t)-R0 = Extension

v= constant velocity

k= spring constant

f(t) = force

Kindly, help me understand if I am going right.

I also have a brief query on the use of dielectric constant( in the

configuration file).

Is it wise to use a dielectric of 80 for water instead of performing the

simulation in water box ?

Will I have to compromise on a significant contribution to energy in doing

so?

Please comment.

Thanks in advance.

Sincerely,

Ramya Gamini

**Next message:**Pijush Ghosh: "RE: force calculation during to conformational change"**Previous message:**Gaurav Sharma: "force calculation during to conformational change"**Next in thread:**Peter Freddolino: "Re: Computing Potential of Mean Force --SMD-cv"**Reply:**Peter Freddolino: "Re: Computing Potential of Mean Force --SMD-cv"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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