Computational Cluster Programs
Chemistry and Chemical Engineering Software on ATS-Hosted Clusters
Software Versions Available on ATS-Hosted Clusters
| Application | Hoffman2 | Cardio | CNSI2 | Hydro | Neutrino |
| Amber | 10 | 8, 9 | |||
| Babel | 1.6 | ||||
| CP2K | 2.0.1 | ||||
| CPMD | 3.13.2 | ||||
| GAMESS | 12 JAN 2009 (R1) | ||||
| Gaussian | 09 A.02, 03 C.02 | 03 C.02 | |||
| GaussView | 5.0, 3.09 | ||||
| GRACE | Yes | Yes | |||
| GROMACS | 4.0.5 | 3.3 | |||
| Jmol | Yes | ||||
| LAMMPS | 7Sep09 | ||||
| Molden | 3.8 | ||||
| Molpro | Yes | ||||
| NAMD | 2.6b1 | ||||
| NWChem | 5.1.1 | 5.0 | |||
| Q-Chem | 3.0.0.6 | 3.0.0.6 | |||
| Quantum ESPRESSO | 4.1.1 | 3.1.1 | |||
| RasMol | 2.7.1 |
Software Package Information and Documentation Links
| Application | Brief Description | Supported | From | Documentation |
| Amber | A suite of programs for use in molecular modeling and molecular simulations. | No | AMBER Development Group |
- How to run on ATS-Hosted Clusters
- Tutorials - Amber 10 Manual |
| Babel | A program to convert between a number of different file formats currently used in molecular modeling, chemistry, solid-state materials, biochemistry, and related areas. | No | Open Babel Project |
- How to run on ATS-Hosted Clusters
- Babel Man Page |
| CP2K | A program that performs atomistic and molecular simulations of solid state, liquid, molecular and biological systems. | No | CP2K Project |
- How to run on ATS-Hosted Clusters
- CP2K Input Reference |
| CPMD | A plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. | No | CPMD Consortium |
- How to run on ATS-Hosted Clusters
- CPMD Manual |
| GAMESS | An electronic structure analysis package. | No | Gordon Research Group |
- How to run on ATS-Hosted Clusters
- GAMESS Documentation |
| Gaussian | Ab initio Quantum Chemistry Software. | No | Gaussian, Inc. |
- How to run on ATS-Hosted Clusters
- Gaussian 09 User's Reference - Gaussian 09 Release Notes (pdf) |
| GaussView | A graphical user interface for preparing input to, submitting, and viewing results from the Gaussian program. | No | Gaussian, Inc. |
- How to run on ATS-Hosted Clusters
- GaussView 5 Reference |
| GRACE (Geometric Real-space Analysis of Crystal Epitaxy) | A program for analyzing the epitaxial relationship between a crystalline substrate and specific contacting planes of a crystalline overlayer. | No | A collaboration between Lian Yu of the Eli Lilly Co. and the Ward research group, Inc. (NYU) | - How to run on ATS-Hosted Clusters |
| GROMACS | A versatile package to perform moledular dynamics. | No | The GROMACS team | - How to run on ATS-Hosted Clusters |
| Jmol | An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. | No | Jmol Project |
- How to run on ATS-Hosted Clusters
- Jmol Documentation - Jmol Wiki |
| LAMMPS | LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator, is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). | No | LAMMPS Molecular Dynamics Simulator |
- How to run on ATS-Hosted Clusters
- LAMMPS Documentation |
| Molden | An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. | No | Radboud University Nijmegen Center for Molecular and Biomolecular Informatics (CMBI), Netherlands |
- How to run on ATS-Hosted Clusters
- Molden Home Page |
| Molpro | A complete system of ab initio programs for molecular electronic structure calculations. | No | H.-J. Werner and P. J. Knowles |
- How to run on ATS-Hosted Clusters
- Molpro User's Manual |
| NAMD | A parallel molecular dynamics code, based on Charm++ parallel objects, designed for high-performance simulation of large biomolecular systems. | No | Theoretical and Computational Biophysics Group, University of Illinois, Urbana-Champaign |
- How to run on ATS-Hosted Clusters
- Tutorial - NAMD User's Guide |
| NWChem | Computational Chemistry Package. | No | - PNL Environmental Molecular Sciences Laboratory |
- How to run on ATS-Hosted Clusters
- NWCHem User Documentation and Reference Manual |
| Q-Chem | An ab initio electronic structure program capable of performing first principles calculations on both ground and excited states of molecules. | Yes | Q-Chem, Inc. |
- How to run on ATS-Hosted Clusters
- Q-Chem User Guides |
| Quantum ESPRESSO | An integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale, based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). | No | DEMOCRITOS National Simulation Center (Trieste) and partners |
- How to run on ATS-Hosted Clusters
- Quantum ESPRESSO User Guide |
| RasMol | A molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. | No | Bernstein + Sons |
- How to run on ATS-Hosted Clusters
- RasMol Home Page - RasMol 2.7.3 Manual |
| XMD | A program for performing molecular dynamics simulations, especially for the simulation of metals and ceramics. | No | the XMD Project |
- How to run on ATS-Hosted Clusters
- XMD Documentation |
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