Applications/Packmol

Application Details

• Description: 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.
• Version: 18.169 (compiled with intel/2018)
• Modules: packmol/intel/18.169
• Licence: Open source (Github)

Introduction

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.

Usage Examples

Interactive session

[username@login01 ~]$ interactive
salloc: Granted job allocation 1211823
Job ID 1211823 connecting to c095, please wait...
[username@c095 ~]$ module load packmol/intel/18.169
[username@c095 ~]$ packmol < mixture.inp

################################################################################

 PACKMOL - Packing optimization for the automated generation of
 starting configurations for molecular dynamics simulations.

                                                              Version 18.169

################################################################################

  Packmol must be run with: packmol < inputfile.inp

  Userguide at: www.ime.unicamp.br/~martinez/packmol

  Reading input file... (Control-C aborts)
  Seed for random number generator:      1234567
  Output file: mixture.pdb
  Reading coordinate file: water.pdb
  Reading coordinate file: urea.pdbmodule load packmol/intel/18.169
[pysdlb@c095 ~]$ packmol < mixture.inp

  Number of independent structures:            2
  The structures are:
  Structure            1 :water.pdb(           3  atoms)
  Structure            2 :urea.pdb(           8  atoms)
  Maximum number of GENCAN loops for all molecule packing:          400
  Total number of restrictions:            2
  Distance tolerance:    2.00000000000000

Batch Script

#!/bin/bash
#SBATCH -J packmol-job                # Job name, you can change it to whatever you want
#SBATCH -n 1                      # Number of cores 
#SBATCH -o %N.%j.out              # Standard output will be written here
#SBATCH -e %N.%j.err              # Standard error will be written here
#SBATCH -p compute                # Slurm partition, where you want the job to be queued 
#SBATCH -t=20:00:00               # Run for 20 hours
#SBATCH --mail-user=your email    # Mail to email address when finished

module purge
module load packmol/intel/18.169
packmol < mixture.inp

Next Steps

• http://m3g.iqm.unicamp.br/packmol/home.shtml

Modules | Main Page | Further Topics