Molecular Dynamics Simulations
RAPTOR® is an Open-Source software package for molecular dynamics simulations of chemical reactions in condensed phase. It is developed by the research group of Prof. Gregory A. Voth at Department of Chemistry, The University of Chicago. RAPTOR® stands for Rapid Approach for Proton Transport and Other Reactions.
Chemical reactions are founded in quantum dynamics. This naturally suggests quantum mechanical simulation methodologies (e.g. ab initio MD or QM/MM), which explicitly simulate the electronic structure, as the ideal method to approach reactive systems. However, the computational expense of these methods strongly limits their applicability to anything but the smallest systems. This has led to the development of reactive molecular mechanics models, such as Multiscale Reactive Molecular Dynamics method (MS-RMD) developed by the Voth group, which faithfully emulate reactive electronic structure through dynamic bonding. Properly parameterized reactive methods such as MS-RMD have the ability to efficiently capture chemical reactivity at a fraction of the computational cost.
The MS-RMD methodology is implemented by the Voth group in RAPTOR® as a plug-in package to LAMMPS, which is a popular molecular dynamics code developed by the Sandia National Laboratory. Therefore, RAPTOR® is compatible with mosft of the features and functions of LAMMPS and can be used for large-scale simulations over hundreds CPU cores via MPI.
Proton transport via Grotthuss shuttling mechanism (changes of elctronic structures)
RAPTOR® is a free software product for all non-profit purposes. It is released in the Source Code version only, and needs to be compiled within the LAMMPS software, which is also free. To obtain more information and installation instructions for LAMMPS, please visit here. Please note that the distrition and use of LAMMPS is currently under the terms of GPL. Furthermore, the use of RAPTOR® needs to be under a Non-Profit Licensing Agreement with its development team.
To obtain RAPTOR®, please read the Non-Profit Licensing Agreement, download the PDF version of it if you agree to this license agreement. In the downloaded agreement, please provide the information of intended use(s) and licensees, and then please sign it and send a scanned copy to the email firstname.lastname@example.org. After reviewing the request, the developer team will send back an approved agreement back, as well as the source code of RAPTOR®.
The newest release of RAPTOR® (Ver 1.0) is compatible with LAMMPS in version 7Aug19.tar.gz.