restrain lateral movement during ABF

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Wed May 16 2018 - 16:34:48 CDT

Hi all,

I am trying to restrain lateral movement of the ion when it is just outside
the entrance of the channel during ABF calculations. My reaction coordinate
is the distance between the center of mass of the spherical protein and the
ion; it does not coincide with z axis, so I can't use distanceXY. The
protein is spherical, and the outer surface is convex. Is there a colvar
that I can use in such a case to keep the ion in place?

If I were to make a tclBC script that would return the ion inside a sphere
of a small radius located just outside the entrance of the channel, how
would that affect ABF outcome for that window? Will such script interfere
with a similar script that I use to push out salt ions from entering the
channel?

Thank you,

Olga

This archive was generated by hypermail 2.1.6 : Mon Sep 16 2019 - 23:19:42 CDT