VMD-L Mailing List

From: M K (mahyar.karimi20_at_gmail.com)
Date: Tue Nov 17 2015 - 20:18:05 CST

Hello,

I usually load a structure file, such as mol, mol2, pdb, car, lammps data
file.... and then load the trajectory into it. I think with this method,
there should not be a problem :)

On Wed, Nov 18, 2015 at 12:05 PM, Dive, Aniruddha Mukund <
aniruddha.dive_at_wsu.edu> wrote:

> Hi,
>
>
> I am running a simulation in lammps with 8 different types of atoms which
> are clearly defined in the input data file. The simulations are running
> perfectly and I am able to generate the trajectory in xyz format.
>
>
> When I try to open this dump.xyz file in VMD the color of atoms in VMD is
> different. When I check the representation column in display it shows the
> name of elements as labeled from H to O i.e. from 1-8 as I have 8 atoms i
> guess. Also if I try to save the co-ordinates into a pdb file, the output
> pdb file shows different atom name than those were earlier in the data file.
>
>
> Is there any way I can overcome this issue and have the correct name for
> atom type as in the input data file.
>
>
> Regards,
>
> *Aniruddha M Dive*
>
> PhD student
>
> School of Mechanical and Materials Engg.
>
> Washington State University
>