From: Axel Kohlmeyer (
Date: Thu Sep 20 2012 - 07:03:07 CDT

On Wed, Sep 19, 2012 at 11:22 AM, ragesh c <> wrote:
> from
> Ragesh c
> National institute of technology,calicut
> India
> sir,
> i have connected two graphene sheet using Add bond tool of VMD.
> After running in Lammps i checked dump file in VMD and saw that , in the
> connected area(Add bond) the c-c bond looks so flexible and deform compare
> to c-c bonds in original graphene.

that is not a VMD issue. the bond will be as strong or as weak
as you set it to be. you have to check whether your input for
LAMMPS is assigning the proper force constant and whether
this behavior is consistent with the physics of your problem.

> one more thing ..After merging .pdb and .psf file of two graphene
> sheet i just added bond. and created new .pdb and .psf file of final
> structure . then i again loaded .pdb and .psf file of final structure , i
> expected final structure will be single unit. but when i used move fragment
> tool to move final structure , each graphene sheet acted as seperate
> fragment and bond between them(which i added using Add bond tool) got
> elongated....i jus wonder , there is some way to creat solid bond between
> two structures

VMD won't recognize that you have connected two fragments
unless you tell it to reanalyze the molecule.


> regards

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