From: Axel Kohlmeyer (
Date: Wed Aug 01 2012 - 06:20:08 CDT

On Wed, Aug 1, 2012 at 11:45 AM, ragesh c <> wrote:
> from
> Ragesh c
> National institute of technology,calicut
> India
> sir,
> 1. i want to generate .pdb and .psf file of graphene
> from VMD (nanotube builder). can you suggest some web page to study about
> it?. or if any one know how to generate .pdb and .psf file of graphene
> generated by nanotube builder of graphene , please help me....[I know how to
> generate data file for lammps input (topo writelammpsdata xxx.txt), but i
> need pdb and .psf file ]..

the VMD users guide explains how to save coordinates and structures
in different file formats. mind you, that does not mean that those files
have the _complete_ information needed for MD simulations. sometimes
this would need to added or generated. e.g. through Tcl scripting or
using tools like psfgen

> 2.Actually i want to merge two graphene structure .
> but for that VMD ask .pdb and .psf file of the two graphene to be merge.
> do any one know how to merge 2 structure generated by VMD without using
> .pdb file ans .psf file.

yes. the topotools plugin (which you already use for writing out
lammps data files) can do that. it is described in the topotools
documentation. again, VMD only uses and writes out information
that you provide in the first place. it is *your* responsibility to
make sure that the information is complete and that the resulting
files are meaningful. all the VMD or its plugins can do is to make
sure the files are written in the correct format. VMD has (by choice)
no understanding of simulations and thus will simply do what
you tell it do, regardless of whether it is meaningful or not.


> thanks

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.