Longleaf Frequently Asked Questions (FAQs)
Description: How do I get an account on Longleaf (or Dogwood)? What are the details of the new filesystem location(s)? Why aren’t `/netscr` nor `/lustre` present on Longleaf? What is the queue structure on Longleaf? How do I transfer data between Research Computing clusters? How do I transfer data onto a Research Computing cluster?   1. […]
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Getting Started with Globus Connect
Description: Below are the individual steps with example screenshots regarding the setup of your Globus login account, accessing our UNC Globus Collection named “UNC, Research Computing, Datamover” (or uncch#unc-rc-dm).   There is an optional installation and configuration of your personal Globus Connect client. Globus addresses deficiencies in secure copy requests by automating large data transfers, by resuming […]
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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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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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Where can I find NWChem software?
Description: Where can I find NWChem software? NWChem is a comprehensive mass-parallel computational chemistry package available on both the KillDevil cluster. More about NWChem Research Computing home page    
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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 – 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 – Materials Studio
Description: Overview Materials Studio® is a software environment that brings the world’s most advanced and validated materials simulation technology to desktop computing, solving key problems throughout the R&D process. Offering advanced visualization tools and access to the complete range of computational materials science methods, Materials Studio is designed for structural and computational researchers in chemicals and […]
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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 – 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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