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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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 – PyMOL
Description: Table of Contents Overview Setting up your Environment and Invoking Links Additional Help Overview PyMOL is a molecular viewer, render tool, 3D molecular editor developed in the spirit of RasMol and OpenRasMol and intended for visualization of 3D chemical structures including atomic resolution X-ray crystal structures of: proteins, nucleic acids (DNA, RNA, & tRNA), and […]
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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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