From: Valerio Sorichetti (valeriosorichetti_at_gmail.com)
Date: Mon Jul 10 2017 - 10:32:44 CDT

Ok, understood. I will take a look at these tools then.

Thank you very much,
Valerio

2017-07-10 16:46 GMT+02:00 Axel Kohlmeyer <akohlmey_at_gmail.com>:

> 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.
>