VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 10 2012 - 18:15:16 CDT

On Tue, Apr 10, 2012 at 6:24 PM, winardi, erik <egw24_at_yahoo.com> wrote:
> Hi VMD users,
>
> I have a question on writing lammps data.
> I have a .car file which contains phenol and formaldehydes molecules.
> In my .car file the C type of the phenols are different from the C type of
> the formaldehydes (C and C1).
> However, when I tried to use topotools to write for lammps input, all the C
> become one type of atom (one ID no.).
> Could I write the C as two ID no. using topotools such as atomID = 1 for C
> of phenol and atomID = 2 for C of formaldehydes, or do I have to do it
> manually ?

the topotools plugin depends on the information that is being fed to it.

atom types for example are based on the string that is stored
in the "type" property in each atom. you have to make sure that
your .car file contains the correct information and it may depend
on how this information is communicated to VMD through the
corresponding plugin. e.g. from what you describe, it may be
possible, that you are looking at the "name" information and
not "type". as far as i know, the carplugin does read the provided
type information. so please check your file and then check what
information VMD does extract from it and how it is assigned
to the various VMD internal atom properties.

cheers,
    axel.

>
> Thanks,
> Erik Winardi 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.