VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Apr 22 2016 - 05:18:28 CDT

On Fri, Apr 22, 2016 at 5:26 AM, ehsan shahini <ehsan.shahiny_at_gmail.com>
wrote:

> Dear all;
> I have a lammps trajectory file that contain 4 atom type and i dump that
> file by this command:
> Dump 1 all atom dump.lammpstrj
> Now when I open this file with vmd all atom types have same diameter. I
> want to every atom type has a unique diameter relating to its mass, how can
> i do that?
>
by default VMD cannot do anything about this, because it is lacking the
information. all that VMD knows about your different atoms is the type (a
number) and the coordinates. there are basically ​two options that are
straightforward to do what you want:

1) in LAMMPS you can write out a custom dump instead of an atom-style dump
and make the dump include the "element" property, where you can assign
element names to each atom type via dump_modify. VMD will then use these
element names to assign element specific atom radii from an internal table
of atom radii.

2) in VMD you can use the Tcl script interface to assign custom radii like
this (off the top of my head and untested):

set sel [atomselect top "name 1"]
$sel set radius 1.5
$sel delete

​set sel [atomselect top "name 2"]
$sel set radius 1.1
$sel delete
​
​set sel [atomselect top "name 3"]
$sel set radius 1.7
$sel delete
​
​set sel [atomselect top "name 4"]
$sel set radius 1.3
$sel delete
​

​axel.​

> Thanks
> 

-- 
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.