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Laboratory for Molecular Simulation
Director: Michael B. Hall Manager: Lisa M. Pérez
Phone: (979) 845-9384Fax (979) 845-2971Rm. 2109 Chemistry
e-mail: mouse@chem.tamu.edu

Welcome to the Laboratory for Molecular Simulation (LMS)

The Laboratory for Molecular Simulation (LMS) brings molecular modeling and computational chemistry closer to the experimental scientist by offering training to both new and advanced users. Advanced modeling software is available for researchers at Texas A&M University to perform quantum calculations on small molecular or solid systems and molecular mechanics/dynamics modeling for large systems such as proteins, DNA, nanomolecules, polymers, solids, and liquids. The LMS also provides support for faculty that wish to incorporate molecular modeling in their course material.

LMS Computer Lab located in Room 2109 Chemistry available for Courses and Research
20 Sun Ultra 20 Linux Workstations acquired through the Sun Academic Excellence Grant

Publications and/or presentations that result from the use of the software and/or hardware provided by the LMS needs to include the following statement in the acknowledgments: We would like to thank the Laboratory for Molecular Simulation at Texas A&M University for providing software(, support, and computer time).

WORKSHOPS - The LMS offers, free of charge, three types of workshops throughout the year: 1) Linux, 2) Molecular Modelling, and 3) Quantum Mechanics Short Course. For more information please see the workshops link to the left. Most of the programs available through the LMS are only available on Linux based machines, therefore, the Linux workshop is a pre-requisite for all other workshops.
HARDWARE - The LMS has 16 Dell Precision T3420 SFF, quad-core xeon processor workstations in the computer lab in room 2109 chemistry. To obtain an account you must complete the Linux workshop or have a VERY strong background in Linux or UNIX. For information or an account on one of the LMS computers, please contact Lisa M. Pérez
SOFTWARE - The LMS has a wide variety of molecular modelling software available. Below is a list of each program with a very brief description of it's purpose. If you are interested in obtaining access to this software, want to test a program/module that we currently do not have a license for, or simply have questions about the software, please contact Lisa M. Pérez.
ADF/ADF-BAND - ADF Package, by SCM is package is software for first-principles electronic structure calculations. ADF is used by academic and industrial researchers worldwide in such diverse fields as pharmacochemistry and materials science. (Linux IA64)
AMBER - AMBER, by David Case at The Scripps Research Instititute and collaborators, is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. (IRIX, AIX, Linux, Windows, and MacOS X)
AOMix - AOMix is a user-friendly Windows software package for molecular orbital (MO) analysis and spectra simulation from results obtained from the following software packages: ADF, GAMESS, Gaussian, HyperChem, Jaguear, MOPAC, Q-Chem, Spartan, and ZINDO. (Windows)
CHARMm - CHARMm (Chemistry at HARvard Macromolecular Mechanics) is a highly regarded and widely used simulation package for small organic molecules, proteins, DNA, and RNA, which combines standard minimization and dynamics capabilities with expert features including normal mode calculations, and correlation analysis. (IRIX, Linux, and Windows)
Dalton - Dalton QCP is a powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2, MCSCF or CC wave functions. (emphasis on magnetic and electric properties) (IRIX and Linux)
Discovery Studio - A user-friendly graphical molecular modelling program developed by Accelrys Inc., that incorporates a variety of useful molecular modelling codes specifically designed for biological systems. (Windows and Linux)
Gaussian 03 (G03) - A suite of programs to perform semi-empirical and ab initio molecular orbital calculations on Linux/UNIX based machines (IRIX, AIX, Linux, MacOS X, and Windows)
GaussView - The GUI interface to Guassian 03. This program is used to assist the user in setting up calculations, and to visualize results (optimized geometries, molecular orbitals, potential surfaces, vibrational modes, etc. ) (IRIX, AIX, Linux, and Windows)
Materials Studio - A Windows based program designed by Accelrys Inc. for the material sciences. The newest developements of the materials science modules available in cerius2 will only be found in materials studio. Many of the internal programs also run on Linux. (Windows and Linux)
Molden - A graphical program that will allow users of a wide variety of molecular modelling codes (including G98) to visualize their results. (IRIX, AIX, Windows, MacOS X and Linux)
MOLEOnline - MOLEOnline provides an interactive web-based tool to found and analyze molecular channels, tunnels and pores. (on-line)
MOLPRO - A complete system of ab initio programs for molecular electronic structure calculations with an emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. (IRIX, AIX, and Linux)
Q-Chem - A modern ab initio, electronic structure program package, capable of performing first principles calculations on the ground and excited states of molecules. (IRIX)
Quanta - A graphical molecular modelling program that has historically been used for life science calculations (CHARMM) and X-ray crystallography, but is currently developed with advanced tools for macromolecular X-ray crystallographers. (IRIX and Linux)
SPOCK - A full-featured molecular graphics program developed by Dr. Jon A Christopher while in the lab of Thomas O. Baldwin of the Department of Biochemistry & Biophysics at Texas A&M University. Spock has been designed from the ground up to be powerful, flexible and most of all, easy to use. (IRIX)
TINKER - The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as AMBER94/96, CHARMM27, MM2(1991), MM3(2000), OPLS-AA and OPLS-UA. (IRIX, Linux, and Windows)

CLASSES - The LMS computer lab is available for use by professors who wish to include molecular modelling in their course material. The LMS will provide the hardware, software, and training necessary for the students and professor. To use the lab for a course, please contact Lisa M. Pérez
PUBLICATIONS - Publications in peer reviewed journals result from collaborative efforts with the LMS and through the support provided to research groups that wish to use the molecular modeling tools available through the LMS. List of publication that have resulted from research performed in the LMS