VMD-L Mailing List

From: Pavan Miriyala (pavan.kumar9111_at_gmail.com)
Date: Tue Mar 18 2014 - 10:47:37 CDT

Hello all,
       I made a single layer graphene using Nano-builder and SiO2 using
Inorganic builder. But, when merging these two structures. I faced an error
like this*"MOLECULE DESTROYED BY FATAL ERROR" and the exciting psf is in *
*charmm **format but it need x-plor format. *
*Then I tried to write psf using the command **"animate write psf x-plor
graphene.psf" as given in the psfgen user ** guide,But then I got a psf
file named x-plor. *

*I fixed it by using these commands *

mol new graphene.psf waitfor all
mol addfile graphene.pdb waitfor all

set sel [atomslect top all]
$sel set segid SHT

animate write psf graphene-xplor.psf waitfor all
animate write pdb graphene-xplor.pdb waitfor all
  But, when i tried to convert the merged pdb file to lammps-data file.
In the data file,

 0.000000 0.000000 xlo xhi

 0.000000 0.000000 ylo yhi

 0.000000 0.000000 zlo zhi

 these are the dimensions.
And I'm getting errors while executing.

Thanks & Regards,
Venkata Pavan Kumar. Miriyala
pavan.kumar9111_at_gmail.com,
contact number: +91-9032307746