VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu May 11 2023 - 16:52:32 CDT

Hello Gabby,
Smoothing your images creates this artifact because of the "spinning" motion of your methyl hydrogen atoms. When that motion is averaged out it will look like a flower blooming.
That is what I have seen in the past.

best
brian

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Gabby Leonard <gabbyleonard94_at_gmail.com>
Sent: Thursday, May 11, 2023 12:54 PM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Trajectory Smoothing and length of hydrogen bonds

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