Scientific Application – GROMACS
Description: Table of Contents Overview Setting up your Environment and Invoking Notes for Usage Links Recommended Citations Additional Help Overview GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that […]
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Scientific Application – Babel
Description: Table of Contents Overview Setting up your Environment and Invoking Notes Links Additional Help Overview Babel is a program designed to interconvert a number of file formats currently used in molecular modeling and computational chemistry. It is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. […]
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Scientific Application – PLINK
Description: Overview PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely an analysis of genotype/phenotype data, so there is no support for steps prior to this. Through integration with gPLINK and Haploview, there is some […]
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Scientific Application – Sybyl
Description: Overview Note: You must be a “tcsh” or “csh” user to benefit from the full functionality of this package. Sybyl provides the front end for comprehensive tools for molecular modeling such as structure building, optimization, visualization of structures and associated data. Additional modules of Sybyl can be added to basis Sybyl to enhance its capability. […]
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Research Computing Programming Tools
Description: Table of Contents Overview General Information Specific Applications Additional help Overview Programming compilers and utility libraries are integral parts of Research Computing resources. FORTRAN 77/90/95, gcc, Intel C and C++ compilers are available for compiling codes to run serial and/or parallel jobs. Some of the compilers are local to the machines. There are also a […]
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Scientific Application – Schrodinger
Description: Table of Contents Overview Setting up Environment and Invoking from a Research Computing Server Installing Locally on a Windows Machine Notes Links Additional Help Overview Schrodinger is a suite of molecular modeling packages that take advantage of the latest technological advances in computational chemistry. Jaguar, the high-performance ab-initio quantum mechanics application, and MacroModel, the most […]
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Scientific Application – NWChem
Description: Overview 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 […]
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Scientific Software Applications
Description: The Research Computing group offers a wide variety of scientific software applications and tools for researchers on campus. These software applications are available for many of the Research Computing servers. Selecting any of the applications below will lead you to a listing of the information provided by the Research Computing group about that application, including […]
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Scientific Application – CPMD
Description: Overview The CPMD code is a plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. Its first version was developed by Jurg Hutter at IBM Zurich Research Laboratory starting from the original Car-Parrinello codes. During the years many people from diverse organizations contributed to the development of the code and of […]
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Gaussian: Tutorial on Water Single Point Energy and Scripts
Description: Introduction You can use a script to create and save a Gaussian file based on restricted Hartree-Fock calculations on a 6-31G(d) basis set for water single point energy. Tutorial Steps Use your favorite editor to create a script file with the following lines and save the file as “spe_hf_6-31g-3”. Water molecule is described in the […]
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