VMD-L Mailing List

From: Gabby Leonard (gabbyleonard94_at_gmail.com)
Date: Thu May 11 2023 - 14:54:23 CDT

Hello,

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.

Thanks,
Gabby


frame1.PNG frame2.PNG