VMD-L Mailing List

From: Albert (mailmd2011_at_gmail.com)
Date: Wed Aug 09 2017 - 12:25:55 CDT

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.

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
> <mailto: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
>> <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.
>
>
>
>
>
> --
> 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.