PDynamo

Introduction

pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions. pDynamo is written in a mixture of Python and C and complements the existing version of Dynamo, now denoted fDynamo, that is written in Fortrans 90 and 95.

The current release version of pDynamo has the following capabilities:

• A density functional theory QC method employing Gaussian basis sets.
• Semi-empirical QC methods of the MNDO type, including AM1, MNDO, PDDG, PM3 and RM1.
• Support for some standard MM force fields, including AMBER, CHARMM and OPLS-AA.
• Hybrid QC/MM methods using any combination of the QC and MM potentials implemented in the library.
• Coupling to third-party QC programs.
• Energy calculations.
• Geometry optimizations.
• Transition state searches.
• Reaction path calculations.
• Normal mode analyses.
• Property calculations, such as charges and dipoles.
• Molecular dynamics simulations.
• Monte Carlo simulations.
• Various "soft" geometrical constraints.
• The ability to handle various common molecular file formats.
• Miscellaneous analysis tools.

Installed version

The currently installed version of pDynamo is 1.9.0.

Using pDynamo on the Cluster

Before you can use pDynamo on the cluster, its necessary to load its corresponding module. You can do that with the command:

module load pDynamo/1.9.0

Since pDynamo needs yaml, you need to load a version of Python which supports yaml to avoid errors. If you want to use e.g. version 3.5.2, you can simply do that by using the command:

module load Python/3.5.2

Loading pDynamo will set the following environment variables:

Environment variable	Path
$PDYNAMO_ROOT	/cm/shared/uniol/software/pDynamo/pDynamo-1.9.0
$PDYNAMO_PARAMETERS	$PDYNAMO_ROOT/parameters
$PDYNAMO_SCRATCH	$WORK
$PDYNAMO_STYLE	$PDYNAMO_ROOT/parameters/cssStyleSheets/defaultStyle.css
$PDYNAMO_PBABEL	$PDYNAMO_ROOT/pBabel-1.9.0
$PDYNAMO_PCORE	$PDYNAMO_ROOT/pCore-1.9.0
$PDYNAMO_PMOLECULE	$PDYNAMO_ROOT/pMolecule-1.9.0
$PDYNAMO_PMOLECULESCRIPTS	$PDYNAMO_ROOT/pMoleculeScripts-1.9.0

IMPORTANT NOTE: The environment variable $PYTHONPATH needs to be set for pDynamo to be functional, otherwise you will get errors. You can do that with the command:

export PYTHONPATH=${PYTHONPATH}:$PDYNAMO_ROOT/pBabel-1.9.0:$PDYNAMO_ROOT/pCore-1.9.0:$PDYNAMO_ROOT/pGraph-0.1:$PDYNAMO_ROOT/pMolecule-1.9.0:$PDYNAMO_ROOT/pMoleculeScripts-1.9.0

Since this line of code is pretty hard to remember, you could add it to your ".bashrc"-file. You will find it in your home-directory. After adding the export-command, you will still need to "refresh" it everytime you load pDynamo. You can simply do that by using the command:

source $HOME/.bashrc

Documentation

More informations about pDynamo can be found here.