Getting Started on KillDevil
Description: Table of Contents Introduction System Information Getting an Account Logging In Directory Spaces Mass Storage Development and Application environment Applications available Software Development Tools Compiling Job Submission Transferring Files Using Tar to Archive FAQs Additional Help Introduction The KillDevil cluster is a Linux-based computing system available to researchers across the campus. With more than 9500 […]
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Scientific Application – Discovery Studio
Description: Table of Contents Overview Setting up Environment and Invoking from a Research Computing Server Installing Locally on a Windows Machine Links Additional Help Overview Discovery Studio is a single unified, easy-to-use, graphical interface for powerful drug design and protein modeling research. Discovery Studio contains both established gold-standard applications (e.g., Catalyst, MODELER, CHARMm, etc.) with years […]
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Scientific Application – BLAST
Description: Overview BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs for exploring the available sequence databases regardless of whether the query is protein or DNA. These well-known applications are written and maintained by the National Center for Biotechnology Information (NCBI). A reworked version of Blast based on the NCBI C++ Toolkit […]
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Scientific Application – SOLAR
Description: Overview SOLAR is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of multiple quantitative traits […]
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Gaussian: Tutorial on Converting Brookhaven Protein Data Bank (PDB) Files to Gaussian Input Files
Description: If a molecular structure is described in Brookhaven Protein Data Bank (PDB) file format, it can be converted to Gaussian input file using the NewZmat command. For example, one can obtain a PDB file for water ( water.pdb) which has the following listing: HEADER REMARK WATER MOLECULE H2O HETATM 1 H UNK 0001 0.000 0.780 […]
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How to restart a Gaussian Run
Description: Table of Contents Using Gaussian Checkpoint Files Commands for reading from the checkpoint file Using Gaussian Checkpoint Files Since the queues on the scientific servers have time limits, the Gaussian calculations may be terminated prematurely due to running out of time. To restart such a prematurely terminated calculation, one can use the checkpointing facilitated via […]
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Scientific Application – GAMESS
Description: Overview The General Atomic and Molecular Electronic Structure System (GAMESS) is a free, general, and parallel (via MPI) ab initio quantum chemistry package. It can compute wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections. Analytic gradients are available for these SCF functions, for automatic geometry optimization, transition state […]
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Scientific Application – Gaussian
Description: Table of Contents Overview Setting up your Environment and Invoking Tutorials Notes for Usage Links Recommended Citations Additional Help Overview Gaussian is capable of predicting many properties of molecules and reactions, including molecular energies and structures, bond and reaction energies, spectroscopic (IR, UV, Raman, NMR) properties, and reaction pathways. Computations can be carried out on […]
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Scientific Application – Amber
Description: Table of Contents Overview Setting up your Environment and Invoking Notes Links Recommended Citations Additional Help Overview Amber (Assisted Model Building with Energy Refinement) is a general-purpose molecular mechanics and dynamics program designed for the refinement of macro-molecular conformations using an analytical potential energy function. All Amber modules execute on our support servers. The program […]
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Scientific Application – NBO
Description: Overview Natural Bond Orbitals (NBOs) are localized few-center orbitals (“few” meaning typically 1 or 2, but occasionally more) that describe the Lewis-like molecular bonding pattern of electron pairs (or of individual electrons in the open-shell case) in optimally compact form. More precisely, NBOs are an orthonormal set of localized “maximum occupancy” orbitals whose leading N/2 […]
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