VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 09 2017 - 09:15:58 CDT

On Wed, Aug 9, 2017 at 10:00 AM, Albert <mailmd2011_at_gmail.com> wrote:

> so there is no solution for this issue currently?
>

​it is not really an issue in my opinion. VMD does what you are asking for
and it is not VMD's problem that you don't like it.

you are free to write a tool that post-processes your trajectory
differently outside of VMD and denoises it more to your liking. however,
finding an algorithm that does what you seem to be looking for, is far from
trivial. i used to have a modification for VMD, that implements a modified
windowed filter that would not just compute an average, but rather would do
a fit to a higher order polynomial. it helps for certain things, but
doesn't resolve the deformation entirely.

axel.
​

>
> 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> 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 http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
> 

-- 
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.