Re: How does NAMD calculate AccumulatedWork when using RMSD colvar?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Apr 12 2018 - 16:14:53 CDT

These labels are explained in the manual:
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html

For "fs" and "fa":
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvar_traj_output

For the energy of the harmonic restraint or any other bias:
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias

Giacomo

On Thu, Apr 12, 2018 at 5:00 PM, Asghar Razavi <asr2013_at_med.cornell.edu>
wrote:

> Hi Giacomo,
>
>
> Thanks very much for the explanation. I was able to reproduce the "
> W_distance_vector" using "fa_d1" and "x0_d1" . I was wondering why not to
> use "d1" for calculations, after all d1 represent the actual
> displacement. Also, I am still confused about what "E_distance_vector"
> and "fs_d1" actually represent. I would appreciate your comments on these--94eb2c0c123a9455630569ad41f4--

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