VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 11 2014 - 07:04:31 CDT

On Mon, Aug 11, 2014 at 5:54 AM, Gamot, Ritchie <R.M.Gamot_at_warwick.ac.uk> wrote:
> Dear Axel,
>
> Thank you for this suggestion. I have in fact done that before submitting the question. But i have this issue of the orientation of the faces. Because each particle will not have its faces the same orientation as with other particles.
>
> I will be able to save this information in file (right now save the centers of each of the particles face) but i have yet to figure out how to do the maths so that i know how to move the second sphere (the twin sphere) so that it would properly represent the face information.

not sure what you are saying here, but for starters, you can just
store the two faces as individual particles and visualize them. if you
want to be more sophisticated, you can compute the vector between the
two faces and then define a scaling factor, multiply the vector with
this factor and add/substract the result to the center and write out
these positions instead.

if you want to choose the displacement after the fact, you could store
your trajectory in LAMMPS format as center and dipole vector and then
use the LAMMPSDIPOLE2ATOMS environment variable to do the scaling and
multi-particle conversion on the fly.
https://sites.google.com/site/akohlmey/software/lammps-plugin

axel.

> I am hoping someone could give me an idea on this dillemma.

>
> Regards,
>
> Chimie
> ________________________________________
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> Sent: 10 August 2014 01:05
> To: Gamot, Ritchie
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: visualizing janus particles in VMD
>
> On Sat, Aug 9, 2014 at 2:24 PM, Gamot, Ritchie <R.M.Gamot_at_warwick.ac.uk> wrote:
>> Good day!
>>
>>
>> I would like to know if anyone can give me an idea on how to represent a
>> two-faced janus particles in VMD?
>
> just use two spheres where each has a different atom type but the same
> radius and place them a tiny bit apart.
>
>
>> I am currently working on janus clusters (saving its particle centre and
>> centre of each of its face). I wonder if there is a way to format my file so
>> that it can be read into VMD and visualize it correctly.
>
> just write them out in a file format that VMD supports. please note
> that for most file formats, VMD expects
> coordinates to be written out in the same order, since from all but
> the first frame, only the coordinate information is read. exceptions
> are only file formats that have an internal indexing (like for LAMMPS)
>
> axel.
>
>>
>> Thank you very much!
>>
>>
>> Regards,
>>
>>
>> Chimie
>
>
>
> --
> 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.