VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 16 2020 - 16:58:45 CDT

in that case, just compute a center of mass trajectory (watch out for
coordinate wrapping/unwrapping) and then write this out in a supported
format (make sure to provide box information) and then compute it as an
atom-atom g(r).

axel.

On Tue, Jun 16, 2020 at 5:15 PM Rameswar Bhattacharjee <
rameswariacs_at_gmail.com> wrote:

> Thank you Axel for your response. I wanted to calculate center to center
> RDF for two molecules. Basically, I want to see how molecules are arranged
> in a solution. I am not sure if VMD has the plugin to do it.
>
>
>
>
>
> On Tue, Jun 16, 2020 at 5:01 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>> The g(r) is at its core an atomic property (assuming point particles to
>> be more specific), so you will first have to define what you mean by a
>> molecule-molecule g(r).
>>
>> Axel.
>>
>> On Tue, Jun 16, 2020 at 4:55 PM Rameswar Bhattacharjee <
>> rameswariacs_at_gmail.com> wrote:
>>
>>> Dear All Users,
>>> I want to see the Molecule-Molecule radial distribution
>>> function instead of the standard atom-atom. I am using a lammps trajectory
>>> and I want to see the molecule-molecule RDF along with the atom-atom. Is
>>> there a plugin in VMD to do So? Any suggestion will be highly appreciated.
>>> Thank you
>>>
>>> --
>>> *Regards*
>>> *Rameswar*
>>>
>>> *********************************************************************
>>> *Dr. Rameswar Bhattacharjee*
>>> Postdoctoral Researcher
>>> University of Delaware
>>> *Newark, DE-19716*
>>> *********************************************************************
>>>
>>>
>>
>> --
>> 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.
>>
>
>
> --
> *Regards*
> *Rameswar*
>
> *********************************************************************
> *Dr. Rameswar Bhattacharjee*
> Postdoctoral Researcher
> University of Delaware
> *Newark, DE-19716*
> *********************************************************************
> 

-- 
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.