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 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.
SGI Computer Lab located in Room 2109 Chemistry
Publications 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) UNIX, 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 unix based SGI
machines, therefore, the unix workshop is a pre-requisite for all other workshops.
more
HARDWARE
- The LMS has 16 SGI O2 workstations in the SGI computer lab in room 2109 chemistry. To obtain an account you must complete the unix
workshop or have a VERY strong background in unix. For information or an account on one of the LMS SGI machines, 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. For detailed information please visit the program links to the left. 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.
(SGI Altix) more
AMBER - AMBER, by David Case at The Scripps Research Insititute and collaborators, is the collective name for a
suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. (UNIX, Linux, Windows, and MacOS X) more
Cerius2 - Cerius2
is a user-friendly graphical molecular modelling program developed by Accelrys Inc. (formerly MSI) that incorporates a wide variety of
popular molecular modelling codes in materials sciences, life sciences and drug design. (SGI) more
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. (SGI) more
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) (SGI and Linux) more
Gaussian 03 (G03) - A suite of programs to perform semi-empirical and ab initio
molecular orbital calculations on unix based machines (UNIX, Linux, MacOS X, and Windows) more
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. ) (UNIX, Linux, and Windows) more
Insight II - A relatively user-friendly graphical molecular modelling program
developed by Accelrys Inc., that incorporates a variety of useful molecular modelling codes specifically designed for biological systems,
including metal containing systems. (SGI) more
MacroModel - The MacroModel program has a large selection of force fields and advanced
methods for conformational analysis, molecular dynamics, and free energy calculations, MacroModel is the most trusted name in molecular
mechanics and is especially well suited for general-purpose molecular mechanics for small and medium-sized organic molecules in both gas and
solution phases. (SGI) more
Materials Studio - A PC 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. (PC) more
Molden - A graphical program that will allow users of a wide variety of molecular
modelling codes (including G98) to visualize their results. (SGI) more
MOLEOnline - MOLEOnline provides an interactive web-based tool to found and analyze molecular channels, tunnels and pores.
(on-line) more
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. (SGI) more
Q-Chem - A modern ab initio, electronic structure program package, capable of performing
first principles calculations on the ground and excited states of molecules. (SGI) more
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. (SGI) more
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. (SGI) more
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. (SGI) more
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 resulting from research performed in the LMS
