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

**Date:** Thu Jul 13 2006 - 07:58:37 CDT

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Dear Peter and Raul,

Thank you for your response.

Thanks so much, the tutorial is really helpful.

In view to Raul's comment, on why not use the full Jarzynski's, I only

presume that solving cumulant expansion is computationally less expensive

than to use the complete expression. May be!!

Also, reconstruction of PMF using expansion to second order fits well with

the actual expression.

Thanks for pointing it out Raul.

May be somebody can better explain.

Sincerely,

Ramya Gamini

*> Dear Ramya,
*

*> the tutorial on pulling decaalanine
*

*> (http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/tutorial-html/index.html),
*

*> and particularly the section on analysis of CV pulling results
*

*> (http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/tutorial-html/node6.html),
*

*> should give you a good template for how to get the PMF out of these
*

*> simulations. (b) looks fine to me. For (c),
*

*>> 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
*

*>>
*

*> Perhaps I'm misreading what you have here, but since the pulling force
*

*> is the force that you're measuring the work of, it seems that you have
*

*> it twice in the equation (once as f(t) and once by the explicit equation
*

*> on the right). The work done by the pulling force at a constant velocity
*

*> is just the integral portion of that equation (derived from a
*

*> substitution of the basic W = int(f(x) dx) when you know x as a function
*

*> of v and t), so you can just plug in the time-based force data you have.
*

*>
*

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

*>> simulation in water box ?
*

*>>
*

*>>
*

*> Having water in your simulation does a good deal more for you than just
*

*> provide a dielectric constant; it also interacts with your solute
*

*> (providing solvation effects), gives you a viscous medium, and provides
*

*> realistic screening effects for short range interactions (where the
*

*> effective dielectric constant is assuredly not 80). There's a good deal
*

*> of ongoing research on implicit solvent models (you can google, for
*

*> example, for implicit solvent model and/or generalized born), but NAMD
*

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