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Re: [lammps-users] Fragments and Melecules analysis/quantification
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Re: [lammps-users] Fragments and Melecules analysis/quantification


From: Steve Plimpton <sjplimp@...24...>
Date: Sat, 19 Aug 2017 07:12:42 -0600

The compute cluster/atom command can group atoms by
clusters and you can dump a cluster ID for each atom
in a dump file snapshot.  All atoms with same ID = one cluster.

Steve


On Fri, Aug 18, 2017 at 11:03 AM, renefbg <renefbg@...6901...> wrote:

Dear all,

Is there a way for LAMMPS (or perhaps VMD) to compute the molecules or fragments existing in each step of the dump file, for example, for the whole simulation?

With a specific determined cutoff distance, could the trajectory file interpret all the fragments/molecules present in each frame and export to a text file or plot it?

As I am currently working on small systems, I can make this evaluation manually, but as the system increases, would be better if the software could supply this info for each timestep.

Thanks.

Rene


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