Introduction

Playmol is a(nother) software for building molecular models.

Its main distinguishing features are:

• Molecules are created with simple scripts consisting of a small set of commands.
• Molecular topology arises naturally when atoms are connected (automatic detection of angles and dihedrals).
• Multiple copies of a molecule are automatically created when new coordinates are defined for their atoms.
• Integration with Packmol [4] provides a way of creating complex molecular systems.
• Generation of LAMMPS [6] and OpenMM [2] files provides a way of performing efficient MD simulations.

The sections of this manual are:

• Installation: provides instructions for Playmol installation
• Playmol Basics: explains the working logic of Playmol
• Commands: describes all Playmol commands
• Sample Scripts: provides sample Playmol scripts

Playmol Users Forum:

https://groups.google.com/forum/#!forum/playmol-users

Online User's Manual:

http://atoms.peq.coppe.ufrj.br/playmol

Copyright

GNU Public License.

Author

Charlles R. A. Abreu (abreu.nosp@m.@eq..nosp@m.ufrj..nosp@m.br)
Applied Thermodynamics and Molecular Simulation Group (ATOMS)
Federal University of Rio de Janeiro, Brazil