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Re: [lammps-users] PBC and topo tool
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Re: [lammps-users] PBC and topo tool

From: Giacomo Fiorin <giacomo.fiorin@...24...>
Date: Fri, 4 May 2018 08:37:07 -0400

Hi Robert, since you're using VMD already it may be useful to use pbc unwrap to bring the coordinates of each pair of to-be-bonded atoms at their nearest-neighbor mutual distance.

If this is not possible, e.g. because you are dealing with a macromolecule that is bonded to one or more of its periodic images, you can use "topo addbond" to manually add bonds for the rest of the TopoTools commands to use.


On Fri, May 4, 2018 at 7:19 AM, Robert Brown <mm229196@...7278...> wrote:
Hi Axel

I'm going use topo tool for guessing bonds and angles of atoms in a system where some particles cross the pbc and seemingly topo tool cannot guess bonds between periodic images. Am I right?
So, what should I do? Please introduce me a convenient way.

Many thanks in advance.

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