RE: SMD Energy

From: Pijush Ghosh (pijush.ghosh_at_ndsu.edu)
Date: Tue May 30 2006 - 12:16:00 CDT

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Dear Li and Sterling

I appreciate your discussion. Well as Li mentioned that the heights of the
peaks depends on the rate of pulling. I have seen similar response for my
system too. I want to share some result on energy with you all so that we
can have some more discussion. I am doing at NPT ensemble. I observed at all
velocities the difference in total energy between final and initial is much
higher than the area under the Force-Displacement curve. Is it expected ?

Pijush Ghosh

PhD Student

Department of Civil Engineering

North Dakota State University

Fargo. ND. 58105. USA

Phone:

701-231-6491(Lab)

701-231-4341(Res)

_____

From: Lewyn Li [mailto:ll2150_at_columbia.edu]
Sent: Tuesday, May 30, 2006 12:01 PM
To: Pijush Ghosh
Subject: Re: namd-l: SMD Energy

Dear Pijush,

This is an interesting question. In my opinion, this depends on
how fast you are pulling the protein. I have found that pulling a protein
from its ends more quickly generally resulted in higher force peaks. If you
then just integrate the force over the extension, you would get a larger
number for a faster pulling. The papers by Lu & Schulten on pulling I27
shows this effect quite nicely.

Also, I believe (but I am not certain) that we need to be
careful about the "energy" in SMD. As the force is calculated from the
moving harmonic potential well, I think the energy of the well should be
taken into account in some way when we speak of the "energy" of the system.

Any advice and suggestions from the SMD experts out there??

LEWYN

On May 30, 2006, at 11:47 AM, Pijush Ghosh wrote:

Dear SMD Experts

In NAMD and from concept of statistical mechanics is it logical to conclude
that the area under the Force-Displacement curve for a protein is equal to
the difference in the initial (t=0) and final (t=T) total energy(bonded +
nonbonded) ?

I would appreciate any discussion on this.