From: Aron Broom (broomsday_at_gmail.com)
Date: Sat Jun 30 2012 - 17:13:59 CDT
I'm fairly certain it means that NAMD performs the alignment each time the
colvar is evaluated (against the model you provide).
I can't see why you would need to pre-align it.
On Sat, Jun 30, 2012 at 12:56 PM, Thomas Albers <talbers_at_binghamton.edu>wrote:
> I am not sure how to understand this sentence from the section on
> Targeted Dynamics: "At each timestep, the RMS distance between the
> current coordinates and the target structure is computed (after first
> aligning the target structure to the current coordinates)."
> Does this mean that NAMD aligns the target coordinates to the model at
> the beginning of the dynamics run, or do I perform the alignment
> before starting NAMD, and the program just calculates forces and
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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