From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Aug 25 2005 - 18:14:34 CDT
You should consult your local physicist, who will point out that based on
F=ma, since none of the atoms in your simulation are experiencing a
consistent acceleration you should expect a net force of zero. If you did
loadforces instead, then only the atoms you are directly applying forces
to would have a nonzero average force, and this would be the negative of
the steering forces you are applying.
On Mon, 22 Aug 2005, LEWYN LI wrote:
> Dear fellow NAMD users,
> I am using the command "loadtotalforces" in NAMD to print the forces on
> selected atoms. I printed out the forces with "loadtotalforces" during a
> simulation where I was stretching a protein at a constant velocity. I fixed
> the N-terminal C-alpha atom and moved the C-terminal C-alpha atom at 0.5
> I originally expected that the atoms near the moving C-terminus would
> experience the applied force more, therefore the forces on them should be
> higher than the atoms in the middle.
> Instead I found that most C-alpah atoms have an average force of
> approximately zero, regardless of their position along the polypeptide
> Has anyone seen something similar in their simulations? Any insight or
> comment would be greatly appreciated. Thank you very much.
> Yours faithfully,
> LEWYN LI
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