VMD-L Mailing List

From: Strahs, Dr. Daniel Bernard (dstrahs_at_pace.edu)
Date: Wed Aug 09 2017 - 10:27:39 CDT

Albert:

Axel spoke correctly. This is not a bug... it's a known and expected property of VMD's algorithm.

As he said, you need to think of more sophisticated algorithms to achieve your desired results.

One possibility is to break your simulation into multiple self-similar segments, and then smooth each segment. You'll have jumps at the boundaries between segments. You might then do a second round, and see if the smoothing of one or two segments smooths over these boundaries.

Please recall that smoothing isn't a replacement for the physically-simulated reality in the computer... so your results will not be physically realistic.

Dan Strahs

Associate Professor, Biology Dept

Pace University, NY

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Albert <mailmd2011_at_gmail.com>
Sent: Wednesday, August 9, 2017 10:00 AM
To: Axel Kohlmeyer
Cc: Vmd l
Subject: Re: vmd-l: vmd smooth trajectory distorted molecule

so there is no solution for this issue currently?

regards

On 08/09/2017 12:40 PM, Axel Kohlmeyer wrote:

On Wed, Aug 9, 2017 at 4:59 AM, Albert <mailmd2011_at_gmail.com<mailto:mailmd2011_at_gmail.com>> wrote:
Hello,

I tick the smooth trajectory function in VMD. However, I noticed that some of my molecule is distorted and looks very weird. I am just wondering how to solve this problem?

?the trajectory smoothing in VMD works by simply applying a window average to atom positions. the observed distortion is a consequence of that and cannot be avoided unless you would implement a much more complex algorithm.

axel.

Thanks a lot

Albert 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.