constant velocity pulling

From: Jamal Zanjani (jamals_at_sabanciuniv.edu)
Date: Thu Mar 31 2016 - 06:04:18 CDT

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Dear All,

I have a question regarding constant velocity pulling via namd. I need to
pull out a ligand from its binding site in a protein to calculate the
binding energy. I realize that for different systems, people are using
various velocity and force constant values in the literature. My question
is how can I adjust pulling velocity and force constant for my specific
system.

Many thanks,
J. Monfared

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