VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Sat Nov 13 2010 - 08:17:24 CST

Hi,all
I do a simulation of graphite with lammps, the type of Carbon atoms in the
file lammps output (lammpstrj or xyz) is "1",

not "C". I hope to change the atom type from "1" to "C" in vmd after loading
these files. So I excuted the following commands,
In the vmd console, it display atom types changed, but "writexyz" output
still type "H". and "mol reanalyze" can't re-analyze rightly
"mol bondsrescalc" failed too.

How should I do? Thank you!

==Test file
10
 generated by VMD
 1 77.785004 67.900002 6.800000
 1 76.556000 68.610001 6.800000
 1 76.556000 70.029999 6.800000
 1 77.785004 70.739998 6.800000
 1 80.245003 67.900002 6.800000
 1 79.014999 68.610001 6.800000
 1 79.014999 70.029999 6.800000
 1 80.245003 70.739998 6.800000
 1 81.474998 68.610001 6.800000
 1 81.474998 70.029999 6.800000

==
==Test commands
mol load xyz test.xyz
[atomselect top "all"] set type C
[atomselect top "all"] get type
mol reanalyze 0
[atomselect top "all"] writexyz test.xyz 

-- 
========================================
Cun Zhang
Ph.D. Candidate
LNM,Institute of Mechanics
Chinese Academy of Sciences
Beijing, 100190, China
Tel:86-10-82544204
http://www.edwardpku.edu.cn/cun
========================================