From: M. A (matabay2010_at_gmail.com)
Date: Thu May 27 2021 - 02:30:54 CDT
Dear All,
I am running MD simulation of ligand and protein interaction with the FEP
method for calculation of free energy parameter. As is mentioned in page 36
of the related tutorial (In silico alchemy: tutorial for alchemical
free-energy perturbation calculations with NAMD), we can measure the
free-energy cost incurred for fading out pseudo bonds by zeroing out
reversibly the associated force constants, until the aforementioned
contribution due to the loss of translational entropy be recovered. Does
anybody know how we can decrease the value of K in the extrabond section of
namd config file? I need the exact script for decreasing K in every window
(for example k=3 to k=0 with dK= 0.09) and simultaneously use it for
measuring free energy in constant lambda.
bests
Maryam
-- Maryam Atabay Ph.D in Nano Computational Chemistry Department of Physics, Sharif University of Technology
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