From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Sat Jul 17 2004 - 03:20:33 CDT
> I want to know if NAMD includes the interaction energy between the two fixed particles
> while reporting the energy values of the whole system?
Depends whether you set "fixedAtomsForces" to 'yes' or 'no'. If set to 'yes' all energies of fixed atoms are included. Default is 'no'.
This is described in page 54 in the manual, but MIND the TYPO there: it says 'on' or 'off' are the possible values, it should be 'yes' and 'no'!
(Correct me if I'm wrong, but I'm pretty sure)
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