VMD-L Mailing List

From: Tabris Chun Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Fri Nov 04 2016 - 10:55:48 CDT

Omg. Brilliant replies! Do not even notice there's an implanted smoothing. Can't wait to try out on my new renders.

Cheers,
Kevin

On 4 Nov 2016, 23:35 +0800, Axel Kohlmeyer <akohlmey_at_gmail.com>, wrote:
> On Fri, Nov 4, 2016 at 10:43 AM, Vermaas, Joshua
> <Joshua.Vermaas_at_nrel.gov> wrote:
> > 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.
>
> FWIW, this "pumping/shrinking" effect can be significantly reduced by
> using a higher order polynomial fitting to the sliding window instead
> of using (0th order) averaging.
>
> this movie uses this and a typical setting here is to average over
> ~100 frames with a 8th or 10th order polynomial.
> https://www.youtube.com/watch?v=lMBRnxbcRH4
>
> for systems with periodic boundaries and particles moving in and out,
> there is another effect that needs to be taken care of. here is an
> example, that has the polynomial filtering, but not the proper
> treatment of PBC:
> https://www.youtube.com/watch?v=6b2WK5rmzBc
> you can see that it is still very busy due to the coarse grained water
> particles (the spheres) jumping in and out of the frame.
>
> this can be addressed by processing the trajectory with a segment wise
> unwrapping, as it is done in this movie:
> https://www.youtube.com/watch?v=lm-dAvbl330
>
>
> all of these visualizations/movies were created with a custom VMD
> version, where i had hacked the trajectory averaging code to use the
> savitzky-golay filter mentioned above.
>
> axel.
>
> >
> > 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
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.