ABF (fwd)

From: Matthew Davies (m.davies_at_mail.cryst.bbk.ac.uk)
Date: Tue Nov 14 2006 - 07:40:30 CST

Dear fellow NAMD users

We are trying to implement the ABF technique to study the dissociation
of a receptor-peptide complex. The receptor binds a single
peptide of 12 amino acids in length. We have applied the technique
by defining the peptide as one centroid and the binding groove of the
receptor as the other centroid and in the simulation we have observed a
clear dissociation of the peptide from the receptor.

Our problem has been in the calculation of the A(xi) values for the
simulation, specifically in selecting the values of xiMin and xiMax
values. At the initial point of our simulation, the two centroids are
approximately 10.4A apart. When we sample the A(xi) values between 10-20A
and 15-20A, we get singificantly higher values for the former. We are
confused by this as we had thought the initial and final points of sampling
would not significantly affect the determined values. Can you suggest at
to why this might occur? I have attached both .dat files as examples.

Best wishes

Matthew Davies

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:49 CST