High Performance Computing Software

Amber is a set of mechanical forcefields for the simulation of biomolecules and also a package of molecular simulation programs. The forcefields are in the public domain and can be used with molecular simulation codes other than the Amber codes.

Distribution
Amber is available on the High Performance Computing group clusters.  

Available Platforms
Windows

Support, Documentation & Training
Email the High Performance Computing group for support.

License Information
Non-commercial, for academic & research purposes only.

COMSOL Multiphysics is a problem-solving simulation environment—based on advanced numerical methods—for modeling and simulating physics-based problems. Enforcing compatibility guarantees consistent multiphysics models.

Distribution
A floating network license is available for the CFD module and for the Microfluidics module. Email the High Performance Computing group for distribution information.

Available Platforms
Windows, Mac, LINUX

Support, Documentation & Training
Email the High Performance Computing group for support and training information.

License Information
Non-commercial, for academic & research purposes only.

Gaussian uses basic quantum mechanic electronic structure programs. This software is capable of handling proteins and large molecules using semi-empirical, ab initio molecular orbital (MO), density functional, and molecular mechanics calculations.

Distribution
Gaussian is distributed by the High Performance Computing group.

Available Platforms
Windows, Mac, LINUX

Support, Documentation & Training
Email the High Performance Computing group for support.

License Information
The NYU Gaussian license only covers PIs at the Washington Square Park campus. We will grant access to you after verifying your WSP affiliation. For access, please email hpc@nyu.edu.

GaussView is a graphical user interface for Gaussian (see above).

Distribution
A desktop license is available upon request. Email the High Performance Computing group for distribution information.

Available Platforms
Windows, Mac, LINUX

Support, Documentation & Training
Reference information is available from the vendor or email the High Performance Computing group for support.

Knitro is a commercial software package for solving large scale mathematical optimization problems. Knitro is specialized for nonlinear optimization, but also solves linear programming problems, quadratic programming problems, systems of nonlinear equations, and problems with equilibrium constraints. The unknowns in these problems must be continuous variables in continuous functions; however, functions can be convex or nonconvex. Knitro computes a numerical solution to the problem—it does not find a symbolic mathematical solution.
Knitro versions 9.0.1 and 10.1.1 are available.

Distribution
Free to NYU faculty, staff, student, researchers.

Support, Documentation & Training
Email the High Performance Computing group for support.

License Information
Non-commercial, for academic & research purposes only.

Maple is a software tool that offers high performance mathematics capabilities with integrated numerics and symbolics. Maple can be used from the command line or with a graphical interface.

Distribution
Email the High Performance Computing group for distribution information.

Support, Documentation & Training
Documentation is available upon request from the High Performance Computing group.

MATLAB is a technical computing environment for high performance numeric computation and visualization. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an easy to use environment without using traditional programming.

Distribution
All faculty, researchers, and students (on any NYU campus) can use MATLAB on their personal computers and laptops. Download the software free of charge.

Support, Documentation & Training
Email the High Performance Computing group for support. Training videos are provided by the vendor: free online courses and more tutorials.

License Information
MATLAB provides access and support for everyone at New York University. MATLAB can be used for non-commercial, academic purposes.

Mathematica is a general computing environment with organizing algorithmic, visualization, and user interface capabilities. The many mathematical algorithms included in Mathematica make computation easy and fast.

Distribution
Mathematica is distributed by the High Performance Computing group. Also faculty and staff can download Mathematica from nyu.onthehub.com.

Support, Documentation & Training
Email the High Performance Computing group for support. Training videos are provided by the vendor:
Wolfram Language Training Courses—Free video courses
Parallel Computing in the Wolfram Language—Free video course

Numerical Algorithms Group (NAG) is the largest collection of algorithms for mathematical, statistical, and data mining problems. The subroutines can be incorporated into code in all languages and used on all platforms. Compilers for Fortran and C are available. Includes: Parallel Library, all Fortran and C libraries, and MATLAB toolbox.

Distribution
Download the software from the NAG website and email the High Performance Computing group for the activation key.

Support, Documentation & Training
Email the High Performance Computing group for support.

License Information
The High Performance Computing group co-licenses NAG with Courant Institute of Mathematical Sciences.

SAS is a software package which enables programmers to perform many tasks, including:

• Information retrieval
  
• Data management
  
• Report writing & graphics
  
• Statistical analysis and data mining
  
• Business planning
  
• Forecasting and decision support
  
• Operations research and project management
  
• Quality improvement
  
• Applications development
  
• Data warehousing (extract, transform, load)
  
• Platform independent and remote computing.

SDTrimSP (Static and Dynamic Trim for Sequental and Parallel computer) is simulation of ion beam sputtering software. SDTrimSP

Distribution
SDTrimSP is installed/compiled on Greene as a module. To have access, please send an email to hpc@nyu.edu, citing the terms of use below and stating that you agree to them.

Support, Documentation & Training
Email the High Performance Computing group for support.

License Information
All NYU employees and students, as well as collaborators who work with NYU can use the software for free for non-commercial use.

• Passing on is prohibited.
  
• No copies are allowed.
  
• All calculated results in publications must be reported
  
• Reference: A.Mutzke, R.Schneider, W.Eckstein, R.Dohmen, K.Schmid, U. von Toussaint, G.Bandelow, SDTrimSP Version 6.00, IPP Report 2019-02
  
• If a user wants a copy of software, contact Andreas Mutzke at SDTrimSP@ipp.mpg.de

Schrodinger enables the solving of problems in Pharmacology, Biotechnology, and Material Science. Schrodinger SiteMap is used in protein structures to identify binding sites.

Distribution
Schrodinger is available on High Performance Computing's Green cluster.

Available Platforms
RHEL 3.9, 4.x, 5.x, 6.x, Windows, Mac

Support, Documentation & Training
Email the High Performance Computing group for support. Training videos are provided by the vendor.

License Information
Schrödinger can be used for non-commercial, academic purposes ONLY. The NYU New York campus has a limited number of licenses for the Biologics Suite (ConfGen, Epik, Jaguar, Jaguar pKa, MacroModel, Prime, QSite, SiteMap), BioLuminate and the Basic Docking Suite.