From: Gabby Leonard (
Date: Thu May 11 2023 - 14:54:23 CDT


I ran a simulation with NAMD and have the rigid bonds parameter activated
for all bonds involving hydrogens. When I play my simulation at normal
speed in VMD there is no problem, however when I apply trajectory smoothing
(window 5), the length of the hydrogen bonds is variable and the side chain
H-bonds don't look normal. I have attached two images to better describe my
problem. Any suggestions on why this may be occurring and how to fix it? I
unwrap most of my simulations, but have tried this with wrapped simulations
and the same phenomenon occurs.


frame1.PNG frame2.PNG