define abf1 and abf2 for CM of water and CM of molecule

From: Manori Indira Jayasinghe (
Date: Mon Dec 19 2005 - 22:53:42 CST

Dear all,
I am studying the free enregy profile of a molecule at water oil
interface. I want to do this simulation in NAMD ABF module. I am very new to namd and
I do working with charmm for several months.I really dont know what to put
for abf1 and abf2 in the abf zcoord module when I define my reaction
coordinates as the z distance between the center of mass of water lemalla
and CM of the molecule. If the reaction cordinate is distance between two
atoms, I know how to do that.That is abf1 is the atom number of one atom
and abf2 is the atom number of the other atom. Please help me to build this
Thank you very much. Manori

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