From: LEWYN LI (ll2150_at_columbia.edu)
Date: Mon Aug 22 2005 - 21:25:44 CDT
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
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.
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