From: Giacomo Fiorin (
Date: Tue Dec 19 2017 - 07:49:40 CST

You could create two VMD selections. For example if the sheet lies
parallel to the XY plane you could use a selection "x >= 0" and another "x
< 0". For each selection you would use the moveby selection command with {
2.0 0.0 0.0 } or { -2.0 0.0 0.0 } as the move vector, respectively.

Bear in mind that once you create such a large gap, you should *not*
simulate the system with the CHARMM force field, for which the PSF file of
the sheet is created by the VMD nanotube plugin, as it assumes fixed
bonds. So the above procedure will only be useful for a figure.

If you do go back to simulating this on LAMMPS (a fair guess given your
earlier questions) then you have better alternatives to CHARMM for this
problem, but it is all but guaranteed that this initial configuration will
be energy-stable.


On Tue, Dec 19, 2017 at 4:56 AM, sumit nagar <> wrote:

> Sir,
> Suppose i have generated a graphene sheet using nano tube builder
> plugin and i want to create a crack of 4 angstroms in the center of it
> . How is this possible interactively or by script(code) writing ?
> Sumit ,Nagar
> M.Tech (Production engg)
> B.E (Production and Ind Engg)
> MCSA 70-290 ,SQL (Oracle z -007)
> ITIL certified ,MCAD 70-306
> GATE 2006,2013

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD