colvars: free energy change with rmsd

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Wed Apr 14 2010 - 00:54:08 CDT

Dear NAMD experts,

I am using the collective variables (colvar) module to calculate the free
energy change as a function of the rmsd of one structure w.r.t another
(reference) structure. Since Adaptive Biasing Force calculations do not
support rmsd, I am employing the Harmonic restraints method. However, unlike
ABF, this method does not yield an output file where one can get the
energies as a function of the colvar. Am I right here? If so, can I get some
alternative suggestions for getting the free energy change as a function of
rmsd?

Thanks,
Neelanjana

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:53 CST