From: stefhoor (fabracht1_at_gmail.com)
Date: Tue Feb 08 2011 - 20:58:39 CST
I have performed an ABF calculation by divinding my reaction path into
numerous intermediate steps. Each interval (0.4 angstrom wide) with a
pull step size of 0.1 A was calculated in a 2 ns window. At the end I
gathered everything with a 0 md step configuration file, which gave me
an integrated pmf file with my entire path. I needed to make an error
analysis of my calculation. I read several papers, most of them were
referenced here in namd's mailing list, and got to the conclusion that
I need to calculate the instantaneous force by adding the
outputSystemForce option within a colvar {} block. Does this mean that
I would have to perform all simulations again in order to compute this
force or is there a way to get them from my current files?
Thank you
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:36 CST