VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Nov 04 2016 - 09:43:31 CDT

Ajasja is exactly right. Depending on how many frames I have loaded, the smoothing can be anywhere from 2-20 frames. What VMD is doing is literally averaging the positions of each atom over a range of frames, which averages out high frequency motions that obscure the slower motions we are interested in. This does have a side effect though, particularly for molecular rings, which will “wink” as they rotate due to the averaging.

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

On Nov 4, 2016, at 4:54 AM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com<mailto:ajasja.ljubetic_at_gmail.com>> wrote:

Hi!

Probably the Trajectory Smoothing Window size (under Graphic representations->Trajectory) was set to something higher than 0.

<image.png>

Best,
Ajasja

On 4 November 2016 at 11:26, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk<mailto:cchan2242-c_at_my.cityu.edu.hk>> wrote:
Dear Users,

I am currently making some MD movies. I looked at some examples on the web (e.g. https://www.youtube.com/watch?v=GSi5-y6NHjY from TCBG UIUC). However, when I made mine, the movement of particles seem very jumpy due to the frame intervals (e.g. https://www.youtube.com/watch?v=uO9-k_HXy0c), especially for the lipid tails. I thought reducing frame intervals could improve but still not working for 20ps per frame, which already made my movie >50000 frames. It looks like the movements have been interpolated or smoothened in some ways.

I know that some of the great movies on webs were made by users here, so I am asking if any post-modifications have been applied to the trajectory. Or you are just using very very small frame intervals.

Thanks in advance,
Kevin
City University of Hong Kong