Question about ABF

From: German Saavedra (
Date: Wed May 09 2007 - 19:09:45 CDT

I want to move a small molecule (27 atoms) along a protein cavity (similar
to a channel) and get energy profiles using ABF. There is 6 types of
reaction coordinate: distance, distance-com, absissa, zCoord, zCoord-1atom,
zCoord-1atom is only for 1 atom and zCoord is useful for the estimation of
transfer free energies between two distinct media. So, which is the best
type of reaction coordinate for my system? Do I have to use zCoord?, could I
use zCoord-1atom? other?.

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