VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jul 10 2017 - 09:46:33 CDT

On Mon, Jul 10, 2017 at 10:05 AM, Valerio Sorichetti
<valeriosorichetti_at_gmail.com> wrote:
> Hello,
>
> I have tried, but for some reason it works on the nanoparticles but not on
> the polymers.
>
> But I think I understand where the problem is. My data are in this format:
>
> Atom_id type x y z
>
> where type=1 for the monomers and type=2 for the nanoparticles.
> The first 100 monomer coordinates represent the first polymer, the second
> 100 the second polymer and so on...
>
> So I think that for vmd there is no way to know that the monomers are part
> of different polymers.
>
> Maybe I have to assign a different type to every polymer? Or is there
> another way?

the best approach is to have a separate molecule id for each separate
molecule and also, it is generally preferable to use the topotools
plugin to generate a .psf file for visualization purposes. that will
better communicate the topology information than having VMD guess it
from the LAMMPS trajectory dump.

https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks

axel.

>
> Thank you very much,
>
> 2017-07-10 15:44 GMT+02:00 Tim Moore <tcmoore3_at_gmail.com>:
>>
>> You can select 'Fragment' for the Coloring Method.
>>
>> On Mon, Jul 10, 2017 at 5:13 AM, Valerio Sorichetti
>> <valeriosorichetti_at_gmail.com> wrote:
>>>
>>> Hello,
>>>
>>> I am simulating a system of bead-spring polymer chains and nanoparticles,
>>> and I was wondering if there is any way to color every polymer chain with a
>>> different (random) color.
>>> The data are in LAMMPS format.
>>>
>>> Thank you very much,
>>> VS
>>
>>
>>
>>
>> --
>> Tim Moore
>
> 

-- 
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.