VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu Apr 19 2018 - 16:12:01 CDT

Question about smoothing a trajectory. I did the explicit water ubiquitin NAMD tutorial under QwikMD tutorials. I am trying to learn about smoothing a trajectory. I load the simulation psf file and then the dcd into VMD. When I play the dcd without smoothing, the waterbox fluctuates normally, but really fast due to the thermal noise. I tried smoothing the trajectory for the water in the representations -> trajectory, but the water box does something strange when smoothing is applied. I tried including two pics, one where the waterbox looks normal during the trajectory, and the second with smoothing, but looks like I couldn't send them. What does smoothing do to the waterbox? I just wanted to see the waters moving more smoothly and slowly instead of jumping around because of thermal fluctuations. I did read something about unwrapping the trajectory, but that didn't really seem to help...unless I did it incorrectly.

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602