zCoord-1atom

From: German Saavedra (gerlord_at_gmail.com)
Date: Tue Apr 10 2007 - 11:24:05 CDT

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Dear NAMD users;
I am trying to run ABF to get energy profiles of a channel, I am using
zCoord-1atom to move an ion along the channel.
I selected as abf1 variable all C types atoms of the protein in a radius
less than 12 (C type and x^2+y^2<144), and I selected as abf2 variable the
ion.
The question is:
Which is the best atoms to select for abf1 variable?
I mean, all the atoms?, or only C type? O type?, O and C types? others?

thanks a lot for your answers,

Germán

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