**From:** Peter Freddolino (*petefred_at_ks.uiuc.edu*)

**Date:** Wed Jul 12 2006 - 02:25:53 CDT

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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:
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*> W(t)= {/ 0 to t(v*f(t)*dt)} - k/2[R(t)- R0 -v*t]^2
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*> where,
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*> / 0 to t =integral 0 to t (sorry!! I had to limit my use of symbols)
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*>
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*> R(t)-R0 = Extension
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*> v= constant velocity
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*> k= spring constant
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*> f(t) = force
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*>
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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
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*> simulation in water box ?
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*>
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*>
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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

does not currently feature any of these models.

Peter

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