PMF Calculation

From: matteo (
Date: Tue Feb 08 2005 - 04:38:20 CST

Recently I have applied SMD to calculate PMF for a 100 aminoacid protein in
water with the aim of accessing the delta G values of mechanical unfolding.

Being the reversible pulling not accessible with my resources i need to know
 how to estimate a priori the error on PMF (2nd order cumulant) for my
From the published data about decaalanine it does not appear so
straightforward to estimante this accuracy.

can someone help me?

p.s. Velocity of pulling for my smd simulation is 0.001 A/fs with spring
force constant K= 7.2 kcal/mol/A^2.

Matteo Pappalardo

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