GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.

Some capabilities include:

• Pure QC simulations - ab initio and SMO.
• Pure MM simulations - using AMBER, CHARMM or OPLS force fields.
• Hybrid QCMM simulations.
• Single point calculations.
• Energy minimization.
• Molecular dynamics.
• Reaction coordinate scanning.
• Umbrella sampling.
• Reaction path calculations - using NEB.

GTKDynamo is available for download for linux and Mac platforms . Please, make sure that you have installed:

• pDynamo
• Matplotlib
• Numpy / Pylab
• Pymol 1.x
• pyGTK
• ORCA, ab initio calculations.

J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI: http://dx.doi.org/10.1002/jcc.23346