Minimization questions...

From: Luis Rosales (
Date: Mon Sep 13 2004 - 19:53:16 CDT


I am starting to play with namd, and from a small search on the list
archives, I have read that one of the parameters to look during an energy
minimization is the "Gradient Tolerance" as this is a good measure of the
system convergence...
However, I still have a couple of very basic questions:

What does the gradient tolerance measure? Is the Gradient tolerance related
to changes on energy, RMS, max derivative?

I wonder if is possible to implement this on a configuration file, to
mimimize the system for X steps or until gradient tolerance is <=Y ???

Thanks for your help,

Luis Rosales

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