|
AMBER
CPMD
Gaussian 03
GaussView
Jaguar
MacroModel
NWChem
QChem
Spartan
VASP
|
|
|
AMBER
|
|
Scripps Research Institute
|
|
AMBER stands for Assisted Model Building with Energy Refinement. AMBER is a family of force fields for molecular dynamics of biomolecules. AMBER is also the name for the molecular dynamics simulation package that implements these force fields.
|
|
amber is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
Hammer
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XB
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XB
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XC
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XC
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XD
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XD
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XJ
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XJ
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XO
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
LION-XO
|
10.0
|
http://ambermd.org/
|
06-Oct-2008
|
|
Versions listed in bold are the default version.
|
|
|
CPMD
|
|
CPMD Consortium
|
|
The CPMD code is a parallelized plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
|
|
CPMD is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
3.9.1
|
http://rcc.its.psu.edu/hpc/software/compchem/CPMD
|
16-Sep-2008
|
|
LION-XB
|
3.9.1
|
http://rcc.its.psu.edu/hpc/software/compchem/CPMD
|
16-Sep-2008
|
|
LION-XC
|
3.9.1
|
http://rcc.its.psu.edu/hpc/software/compchem/CPMD
|
16-Sep-2008
|
|
LION-XD
|
3.9.1
|
http://rcc.its.psu.edu/hpc/software/compchem/CPMD
|
16-Sep-2008
|
|
LION-XJ
|
3.9.1
|
http://rcc.its.psu.edu/hpc/software/compchem/CPMD
|
16-Sep-2008
|
|
LION-XO
|
3.9.1
|
http://rcc.its.psu.edu/hpc/software/compchem/CPMD
|
16-Sep-2008
|
|
Unisys
|
3.9.1
|
http://rcc.its.psu.edu/hpc/software/compchem/CPMD
|
22-Sep-2008
|
|
Versions listed in bold are the default version.
|
|
|
Gaussian 03
|
|
Gaussian, Inc.
|
|
Gaussian 03 is designed to model a broad range of molecular systems under a variety of conditions performing its computations starting from the basic laws of quantum mechanics.
|
|
G03 is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
E.01
|
http://rcc.its.psu.edu/hpc/software/compchem/g03
|
03-Jan-2008
|
|
LION-XB
|
E.01
|
http://rcc.its.psu.edu/hpc/software/compchem/g03
|
03-Jan-2008
|
|
LION-XC
|
E.01
|
http://rcc.its.psu.edu/hpc/software/compchem/g03
|
03-Jan-2008
|
|
LION-XD
|
E.01
|
http://rcc.its.psu.edu/hpc/software/compchem/g03
|
03-Jan-2008
|
|
LION-XJ
|
E.01
|
http://rcc.its.psu.edu/hpc/software/compchem/g03
|
10-Sep-2008
|
|
LION-XO
|
E.01
|
http://rcc.its.psu.edu/hpc/software/compchem/g03
|
03-Jan-2008
|
|
Versions listed in bold are the default version.
|
|
|
GaussView
|
|
Gaussian, Inc.
|
|
GaussView makes using Gaussian 03 simple and straightforward:
* Sketch in molecules using its advanced 3D Structure Builder, or load in molecules from standard files.
* Set up and submit Gaussian 03 jobs right from the interface, and monitor their progress as they run.
* Examine calculation results graphically via state-of-the-art visualization features: display molecular orbitals and other surfaces, view spectra, animate normal modes, geometry optimizations and reaction paths.
GaussView supports all Gaussian 03 features, and it includes graphical facilities for generating keywords and options, molecule specifications and other input sections for even the most advanced calculation types. GaussView makes it simple to set up ONIOM layers, unit cells for Periodic Boundary Conditions jobs, CASSCF active spaces, molecule specifications for transition structure optimizations using the STQN method, and so on. We’ll look at many of them in the following pages.
|
|
gv is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
4.1
|
http://rcc.its.psu.edu/hpc/software/compchem/gv
|
11-Sep-2008
|
|
LION-XB
|
4.1
|
http://rcc.its.psu.edu/hpc/software/compchem/gv
|
11-Sep-2008
|
|
LION-XC
|
4.1
|
http://rcc.its.psu.edu/hpc/software/compchem/gv
|
11-Sep-2008
|
|
LION-XD
|
4.1
|
http://rcc.its.psu.edu/hpc/software/compchem/gv
|
11-Sep-2008
|
|
LION-XJ
|
4.1
|
http://rcc.its.psu.edu/hpc/software/compchem/gv
|
11-Sep-2008
|
|
LION-XO
|
4.1
|
http://rcc.its.psu.edu/hpc/software/compchem/gv
|
11-Sep-2008
|
|
Versions listed in bold are the default version.
|
|
|
Jaguar
|
|
Schrodinger, Inc.
|
|
Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory.
|
|
Jaguar is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
55.011
|
http://rcc.its.psu.edu/hpc/software/compchem/Jaguar
|
11-Sep-2008
|
|
LION-XB
|
55.011
|
http://rcc.its.psu.edu/hpc/software/compchem/Jaguar
|
11-Sep-2008
|
|
LION-XC
|
55.011
|
http://rcc.its.psu.edu/hpc/software/compchem/Jaguar
|
11-Sep-2008
|
|
LION-XD
|
55.011
|
http://rcc.its.psu.edu/hpc/software/compchem/Jaguar
|
11-Sep-2008
|
|
LION-XJ
|
55.011
|
http://rcc.its.psu.edu/hpc/software/compchem/Jaguar
|
11-Sep-2008
|
|
LION-XO
|
55.011
|
http://rcc.its.psu.edu/hpc/software/compchem/Jaguar
|
11-Sep-2008
|
|
Versions listed in bold are the default version.
|
|
|
MacroModel
|
|
Schrodinger, Inc.
|
|
MacroModel is an integrated software system for modeling organic and bioorganic molecules using molecular mechanics.
|
|
MModel is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
90.016
|
http://rcc.its.psu.edu/hpc/software/compchem/macromodel
|
11-Sep-2008
|
|
LION-XB
|
90.016
|
http://rcc.its.psu.edu/hpc/software/compchem/macromodel
|
11-Sep-2008
|
|
LION-XC
|
90.016
|
http://rcc.its.psu.edu/hpc/software/compchem/macromodel
|
11-Sep-2008
|
|
LION-XD
|
90.016
|
http://rcc.its.psu.edu/hpc/software/compchem/macromodel
|
11-Sep-2008
|
|
LION-XJ
|
90.016
|
http://rcc.its.psu.edu/hpc/software/compchem/macromodel
|
11-Sep-2008
|
|
LION-XO
|
90.016
|
http://rcc.its.psu.edu/hpc/software/compchem/macromodel
|
11-Sep-2008
|
|
Versions listed in bold are the default version.
|
|
|
NWChem
|
|
William R. Wiley Environmental Molecular Sciences Laboratory (EMSL)
|
|
NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL). Most of the implementation has been funded by the EMSL Construction Project.
|
|
nwchem is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
xc
|
http://rcc.its.psu.edu/hpc/software/compchem/nwchem
|
11-Sep-2008
|
|
LION-XB
|
xc
|
http://rcc.its.psu.edu/hpc/software/compchem/nwchem
|
11-Sep-2008
|
|
LION-XC
|
xc
|
http://rcc.its.psu.edu/hpc/software/compchem/nwchem
|
11-Sep-2008
|
|
LION-XD
|
xc
|
http://rcc.its.psu.edu/hpc/software/compchem/nwchem
|
11-Sep-2008
|
|
LION-XJ
|
xc
|
http://rcc.its.psu.edu/hpc/software/compchem/nwchem
|
11-Sep-2008
|
|
LION-XO
|
xc
|
http://rcc.its.psu.edu/hpc/software/compchem/nwchem
|
11-Sep-2008
|
|
Versions listed in bold are the default version.
|
|
|
QChem
|
|
Q-Chem, Inc.
|
|
Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods. Q-Chem tackles a wide range of problems in commercial, academic and government laboratories, including:
* Molecular Structures
* Chemical Reactions
* Molecular Vibrations
* Electronic Spectra
* NMR Spectra
* Solvation Effects
Q-Chem provides users with some distinct advantages:
* Fast DFT calculations with accurate linear scaling algorithms
* A wide range of post-HF correlation methods that are efficient and unique
* Quantum calculations extended with QM/MM and molecular dynamics
|
|
qchem is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
3.1-02
|
http://rcc.its.psu.edu/hpc/software/compchem/qchem
|
11-Sep-2008
|
|
LION-XB
|
3.1-02
|
http://rcc.its.psu.edu/hpc/software/compchem/qchem
|
11-Sep-2008
|
|
LION-XC
|
3.1-02
|
http://rcc.its.psu.edu/hpc/software/compchem/qchem
|
11-Sep-2008
|
|
LION-XD
|
3.1-02
|
http://rcc.its.psu.edu/hpc/software/compchem/qchem
|
11-Sep-2008
|
|
LION-XJ
|
3.1-02
|
http://rcc.its.psu.edu/hpc/software/compchem/qchem
|
11-Sep-2008
|
|
LION-XO
|
3.1-02
|
http://rcc.its.psu.edu/hpc/software/compchem/qchem
|
11-Sep-2008
|
|
Versions listed in bold are the default version.
|
|
|
Spartan
|
|
Wavefunction, Inc.
|
|
Spartan is a molecular modelling and computational chemistry application. It contains code for both ab initio and semi-empirical quantum chemistry methods.
|
|
spartan is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
6.129.26
|
http://www.wavefun.com/products/spartan.html
|
06-Oct-2008
|
|
LION-XB
|
6.129.26
|
http://www.wavefun.com/products/spartan.html
|
06-Oct-2008
|
|
LION-XC
|
6.129.26
|
http://www.wavefun.com/products/spartan.html
|
06-Oct-2008
|
|
LION-XD
|
6.129.26
|
http://www.wavefun.com/products/spartan.html
|
06-Oct-2008
|
|
LION-XJ
|
6.129.26
|
http://www.wavefun.com/products/spartan.html
|
06-Oct-2008
|
|
LION-XO
|
6.129.26
|
http://www.wavefun.com/products/spartan.html
|
06-Oct-2008
|
|
Versions listed in bold are the default version.
|
|
|
VASP
|
|
University of Vienna
|
|
VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing. These techniques avoid all problems occurring in the original Car-Parrinello method which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Both techniques allow a considerable reduction of the necessary number of plane-waves per atom for transition metals and first row elements. Forces and stress can be easily calculated with VAMP/VASP and used to relax atoms into their instantaneous groundstate.
|
|
vasp is available on the following HPC machines:
|
|
Machine
|
Version
|
Instructions
|
Last Update
|
|
Hammer
|
-
|
http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
|
06-Oct-2008
|
|
LION-XB
|
-
|
http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
|
06-Oct-2008
|
|
LION-XC
|
-
|
http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
|
06-Oct-2008
|
|
LION-XD
|
-
|
http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
|
06-Oct-2008
|
|
LION-XJ
|
-
|
http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
|
06-Oct-2008
|
|
LION-XO
|
-
|
http://cms.mpi.univie.ac.at/vasp/vasp/vasp.html
|
06-Oct-2008
|
|
Versions listed in bold are the default version.
|
|
