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Re: [lammps-users] bond,angle across boundary from VMD topo
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Re: [lammps-users] bond,angle across boundary from VMD topo

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Mon, 4 Dec 2017 08:58:57 -0500

On Mon, Dec 4, 2017 at 8:07 AM, Yafan Yang <yafan.yang@...7270...3...> wrote:
Dear all,

I am trying to use VMD to generate a graphene structure and output to lammps datafile by topo.

​VMD (and thus topotools) has no integrated facilities to detect/create bonds across periodic boundaries. PBC support in VMD is extremely limited in many ways.
It seems there are some bonds missing across the boundaries in the output datafile. Does anyone know how to add bond to the datafile? Thanks!

​most simulations where class 1 force fields (with explicit bonds etc)​ are used, graphene or carbon nanotubes are generally left immobile and then bonds/angles/etc don't matter, or if they are left mobile, people seem to prefer many-body potentials like Tersoff or AIREBO to represent those compounds, in which case bonds/angles/etc are implicit and thus *must* not be included in the data file at all.




Best regards,
Yafan Yang

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Dr. Axel Kohlmeyer  akohlmey@...12...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.