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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Gaussian: Tutorial on Using LSF Scripts to Automate Jobs
Description: Introduction When Gaussian starts running jobs for relatively big molecules, it requires more disk space in saving some intermediate results during the course of the computation. It is always better to start up the job in scratch space to take advantage of unlimited disk space. In order to avoid moving files back and forth between […]
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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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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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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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Gaussian: Tutorial on Water Single Point Energy and the Command Line
Description: Table of Contents Introduction Setup on the Available Clusters Run Gaussian in scratch space Tutorial Steps Running Gaussian on the Clusters Additional Links Introduction You can use command line execution to create and save a Gaussian input file. Below is an example based on restricted Hartree-Fock calculations on a 6-31G(d) basis set for water single […]
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Research Computing: Contact Us
Description: By Web Complete the web form Submit a Help Request.  In the “Choose the Department or Service you need assistance with” drop-down, select ITS Services then under “Type of Help Needed” drop-down, select Research Computing. In the Problem Description box, describe the problem and specify your operating system (Linux, Windows, etc.), the name/version of the […]
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