Playmol
May 11, 2018 ยท View on GitHub
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 provides a way of creating complex molecular systems.
- Generation of LAMMPS and OpenMM files provides a way of performing efficient MD simulations.
Copyright: GNU Public License.
Author: Charlles R. A. Abreu
Applied Thermodynamics and Molecular Simulation Group (ATOMS)
Federal University of Rio de Janeiro, Brazil
Online Manual
The Playmol User Manual is available at:
http://atoms.peq.coppe.ufrj.br/playmol
Forum
A forum for Questions & Answers about Playmol is available at:
https://groups.google.com/forum/#!forum/playmol-users
Installation
Playmol is distributed as a git repository. To download it, just run:
git clone https://github.com/atoms-ufrj/playmol
To compile the source code and install Playmol in your system, you can do:
cd playmol
make
sudo make install
To update Playmol, enter the playmol directory and execute the following commands (including recompilation and reinstallation):
git pull
make
sudo make install
User's Manual
The Playmol User's Manual is available online here. You can also generate a local version if you have Doxygen (version 1.8 or later) installed in your system. If you do not have Doxygen, you can download and install it by:
wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.11.src.tar.gz
tar -zxvf doxygen-1.8.11.src.tar.gz
cd doxygen-1.8.11/
sudo apt-get install cmake flex bison
mkdir build && cd build/
cmake ../
make
sudo make install
In order to generate the local User's Manual, please go to the playmol directory and execute:
make doc
The manual will be available as a file playmol/doc/html/index.html, which you can open using your favorite web browser.
Using Playmol
Once Playmol is installed, you can execute a series of input scripts by typing:
playmol file-1 [file-2 ...]
This will execute the files in sequence as if they were a unique script. To execute the scripts one at a time, just run playmol multiple times.
Another way of runnig a playmol script is by starting it with the following line and then making it executable (e.g. via chmod +x):
#!/usr/local/bin/playmol
List of Playmol Commands
Here is a complete list of Playmol commands:
| Command | Description |
|---|---|
| define | defines a variable for further substitution |
| for/next | executes commands repeatedly while changing the value of a variable |
| if/then/else | executes commands conditionally or selects between two command sequences |
| atom_type | creates an atom type with given name and parameters |
| mass | specifies the mass of atoms of a given type |
| diameter | specifies the diameter of atoms of a given type |
| bond_type | defines parameters for bonds between atoms of two given types |
| angle_type | defines parameters for angles involving atoms of three given types |
| dihedral_type | defines parameters for dihedrals involving atoms of four given types |
| improper_type | defines parameters for impropers involving atoms of four given types |
| models | defines whether the first attribute of each type is a model name |
| atom | creates an atom with given name and type |
| charge | specifies the charge of a given atom |
| bond | creates chemical bonds and automatically detects angles and dihedrals |
| improper | creates an improper involving four given atoms or search for impropers |
| rigid_body | selects a set of atoms to be marked as a rigid body |
| mixing_rule | defines mixing rules for pairs of atom types |
| extra | creates an extra bond, angle, or dihedral involving given atoms |
| link | links two atoms (and fuses their molecules) without actually bonding them |
| unlink | removes an existing link (and splits the corresponding molecule) |
| build | guesses atom positions from provided geometric information |
| prefix/suffix | defines default prefixes or suffixes for atom types and atoms |
| box | defines the properties of a simulation box |
| velocity | defines parameters for generating Maxwell-Boltzmann atomic velocities |
| align | aligns the principal axes of a molecule to the Cartesian axes |
| packmol | executes Packmol in order to create a packed molecular system |
| write | saves system info in different file formats (including LAMMPS and OpenMM) |
| include | includes commands from another script |
| reset | resets a list of entities together with its dependent lists |
| shell | executes an external shell command |
| quit | interrupts the execution of a Playmol script |
The syntax and behavior of each command is described in the Playmol documentation.
Input Script Examples
Some input script examples are available in the playmol/examples directory.