Packmol

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.

Installation

Step 1

Download it from this page.

Step 2

Expanding the files:

tar -xvzf packmol.tar.gz

This will create a directory called packmol inside which you can find the source code. You can build the executable by:

cd packmol

make

That's it, if no error was reported the packmol executable was built. If you have problems, let the configure script find a suitable compiler for you:

chmod +x ./configure

./configure

Documentation

You can access documents from this page.

Basic user guide

Running Packmol

Once you have compiled and built your input file, run Packmol with packmol < packmol.inp where packmol.inp is the input file

A successful packing will end with something like below:

------------------------------ 

Success!

Final objective function value: .22503E-01

Maximum violation of target distance: 0.000000

Maximum violation of the constraints: .78985E-02

------------------------------

Packmol input file example

Simple packmol input file looks like below:

tolerance 2.0 

output 8000.pdb 

filetype pdb 

structure PE_simple_chain.pdb 

  number 8000 

  inside cube 0. 0. 0. 450. 

end structure