Re: Targeted Molecular Dynamics

From: Aron Broom (
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 <>wrote:

> Hello!
> 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
> rmsds?
> Regards,
> Thomas

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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