Introduction

Moltemplate is a text-based program designed to build molecules for use in LAMMPS simulations. While it was designed with the intention of building complex coarse-grained toy molecular modles, it can be used to build molecules for realistic LAMMPS simulations as well. Moltemplate is capable of representing almost any kind of molecular model or force field that LAMMPS can simulate in the form of moltemplate objects. These objects can be used as building blocks to build new molecular objects whose subunits can be customized. It is even possible to convert existing LAMMPS files into moltemplate format using a python utility, "ltemplify.py".

Usage of moltemplate at the RCC

The package is installed in the directory

/opt/hpc/moltemplate/    

To use the utilities provided by the moltempate software package, please add the following to your $PATH and $PYTHONPATH environmental variables.

If you use bash, add the following to your .bashrc file:

export PYTHONPATH=/opt/hpc/moltemplate/src:$PYTHONPATH
export PATH=/opt/hpc/moltemplate/src:$PATH

If you use cshell, add the following to your ~/.cshrc file:

setenv PYTHONPATH /opt/hpc/moltemplate/src:${PYTHONPATH}
setenv PATH /opt/hpc/moltemplate/src:${PATH}

To test if they are available to you,

  $ which moltemplate.sh
  $ python  ltemplify.py

Both utilities should be found.