VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Dec 30 2022 - 19:16:49 CST

Fatima,

What you are trying to do requires more than a beginner's understanding of
VMD, so you are strongly advised to first practice simpler tasks and
approach this in stages.

VMD is limited by the molfile plugin interface in what per-atom properties
it can import, so the trick with LAMMPSREMAPFIELDS is to disguise one
property as another. I have explained the procedure before here:
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/18844.html

However, if you are not locked into using VMD for visualization, you may
consider using OVITO instead. where this kind of task is *much* more
straightforward to do.

Axel.

p.s.: please keep in mind that atomic forces fluctuate a *lot* during an
MD, so you probably want to use a time averaging fix in LAMMPS to get
smoother data.

On Fri, Dec 30, 2022 at 6:37 PM Fateme Aghaei <f.aghaei.a_at_gmail.com> wrote:

> Hi,
> Hope you have been doing well.
>
> I am new in VMD and I need your help.
> I am going to color a particle of my system based on the time series of
> the force acting on it. The dynamic of the system is simulated by Lammps
> and I have dump files for the positions of the particles and the force.
> where should I load the time series of the force and how can I set VMD to
> color based on it?
> I have found some guides by LAMMPSREMAPFIELDS
> and also Tcl scripts. but I need more detail to know how to apply them.
> I will be thankful if you could help me with these methods or another way
> to color the particle according to the dump file of the force.
>
> Best Regards,
> Fatima
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!8J_MqGEb16tnqzQxELdv0vrCd37A0yesImd6zzdq8PDFwo0_1bZAVAx9l7pQhVj-xpvxsnEffNe817AN4A$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.