VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 09 2017 - 13:00:15 CDT

On Wed, Aug 9, 2017 at 1:25 PM, Albert <mailmd2011_at_gmail.com> wrote:

> I could do this in Gromacs before I load it to VMD. However, the smooth
> the .xtc file has the same problem observed in VMD.
>
​if it applies the same algorithm​ (windowed average of position data),
then it is exactly what you should get.

> Albert
>
> On 08/09/2017 04:15 PM, Axel Kohlmeyer wrote:
>
>
>
> 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.
>
>
> 

-- 
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.