VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Thu May 11 2023 - 16:13:12 CDT

Hi Gabby,

The way trajectory smoothing works in VMD is to visualize the average position for an individual atom across multiple frames. This has the desired smoothing effect to make individual motions less jittery, but it also has the undesired effect of making things that move quickly (like rotating methyl groups) look ridiculous, since the average position is not guaranteed to be in a physically reasonable place. If I am doing analysis, I typically will not use smoothed coordinates, since it edits the coordinates. However, if I’m trying to make a movie that looks good and makes a point, I may use trajectory smoothing and hide hydrogens/aromatic rings (which wink! Its very silly) in visualization.

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Gabby Leonard <gabbyleonard94_at_gmail.com>
Date: Thursday, May 11, 2023 at 5:04 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