Packmol

Overview

Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.

The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.

Version 18.169 is installed.

Restrictions on use

None: MIT license.

Set up procedure

To access the software you must first load the modulefile:

module load apps/intel-17.0/packmol/18.169

NOTE we now recommend loading the module file within your batch scripts.

Running the application

Packmol is not parallelised, you should only run serial jobs.

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
module load apps/intel-17.0/packmol/18.169

packmol < filename.inp

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

See the Packmol web site for usage and examples.