**From:** Gungor Ozer (*gungor.ozer_at_gmail.com*)

**Date:** Sat Apr 05 2008 - 19:10:06 CDT

**Next message:**Yinglong Miao: "Re: vmd-l: How to read specific DCD frames directly in Fortran?"**Previous message:**Peter Freddolino: "Re: vmd-l: How to read specific DCD frames directly in Fortran?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear all,

I've done a series of constant velocity SMD simulations and now trying to

compute the average PMF of these trajectories. As far as I get from the two

Schulten papers ("Calculating potentials of mean force from steered

molecular dynamics simulations" in JCP & "Free energy calculation from

steered molecular dynamics simulations using Jarzynski's equality") and from

the manuals this is done;

1) by first calculating the work => integrate f*v*dt over time elapsed.

2) then by applying the Jarzynski's equality.

My questions:

1) Since any SMD simulation is not perfect, and not exactly following a

constant velocity path, shouldn't we use f*dx in eq.1 with dx being the

exact displacement of the steered particle?

2) f in eq 1 is a vector, how are we supposed to integrate a vector*scalar?

and a different question.

3) I am using TCL script to calculate force vector:

"

set ff [expr $k*($nx*($r0x-$rx)+$ny*($r0y-$ry)+$nz*($r0z-$rz) +

$time*$velocity)]

set fx [expr $ff*$nx]

set fy [expr $ff*$ny]

set fz [expr $ff*$nz]

"

ff being the force derived from the potential given U = 1/2k [ vt - (r-r0)*n

] where r is the current position, r0 is the initial position and n is the

direction vector.

Does my TCL script seem to calculate correct amount of work?

Any help to any of the questions will be much appreciated.

Regards,

Gungor Ozer

Georgia Tech

**Next message:**Yinglong Miao: "Re: vmd-l: How to read specific DCD frames directly in Fortran?"**Previous message:**Peter Freddolino: "Re: vmd-l: How to read specific DCD frames directly in Fortran?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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