Office of Science
FAQ
Capabilities

General Modeling Software

Extensible Computational Chemistry Environment (Ecce)

Ecce, part of the Molecular Science Software Suite, MS3, supports chemists with calculation planning and management, a common interface to multiple computational codes, selection of basis sets, a browsable calculation and chemistry database, management of calculation jobs on networked computers, and visualization of results.

gOpenMol - Version 3.0

gOpenMol is the graphical user interface for OpenMol, for visualizing electrostatic surfaces and grids.

gOpenMol is a program or toolbox for the display of molecules and their properties and the analysis of molecular structures and dynamics trajectories. gOpenMol, as an analysis and display toolbox, can be used for:

  • static display of molecular structures and properties calculated with external programs
  • analysis and display of molecular dynamics trajectories
  • display of molecular orbitals, electron densities
  • electrostatic potentials from programs like GaussianXX
  • electrostatic potentials from the UHBD (University of Houston Brownian Dynamics) and the GRID programs.

The version we now have installed on nwvisus is 3.00. Before one can access gOpenMol, the following alias needs to be defined in your .mycshrc file:

    if ("$HOST" == "nwvisus") then
        alias gopen /files0/gopenmol/bin/rungOpenMol
    endif

To start gOpenMol, enter 'gopen' within a shell window. It is possible to download your own copy of gOpenMol to install on your PC or workstation from the gOpenMol Home Page.

Life Sciences Software - Insight II 97.0

Insight provides an easy-to-use simulation and modeling environment, offering a broad range of scientific application modules. MSC has the selected Insight modules listed below. To access this software, please contact the MSC Consultants by sending e-mail to mscf-consulting@emsl.pnl.gov.

Discover

Molecular mechanics/dynamics

The FDiscover (the FORTRAN version of Discover®) performs energy minimization, template forcing, torsion forcing, and dynamic trajectories and calculates peroperties such as interaction energies, derivatives, mean square displacements. It provides tools for performing simulations under various conditions including constant temperature, constant pressure, constant stress, periodic boundaries, and fixed and restrained atoms.

Analysis

Analyzing molecular dynamics trajectories

The Analysis module is used to display data, especially from molecular conformation analyses, in graphs or molecular animation. Typically, the input data of molecular conformations comes from the Discover program, but this data can come from any source, provided it is formatted in a way that is recognizable to the Insight II program.

Biopolymer

Building macromolecules

The Biopolymer module facilitates the building and modification of peptides, proteins, polysaccharides and nucleic acids. In particular these commands can be used to:

Homology

Making 3D protein models from sequences

Homology is a computer program package that helps you build the structure of a protein when you know only its amino acid sequence and the complete atomic structure of at least one other reference protein.

DelPhi

Electrostatic potential in and around molecules

DelPhi is a software package that calculates the electrostatic potential in and around macromolecules, using a finite difference solution to the nonlinear Poisson-Boltzmann equation. The program allows specification of ionic strength as well as dielectric constants of both the solvent and the molecule of interest.

DMol

Density functional ab-initio code

DMol is a first-principles (ab initio) quantum chemistry software package that performs accurate theoretical calculations on a wide range of compounds, including metal clusters, biological compounds, organometallics, and organic compounds.

Turbomole

Ab-initio code

Turbomole is a general-purpose, ab initio quantum chemistry program package designed for the prediction of molecular energies, structures, spectra, reactivity, and properties.

Material Sciences Software - Cerius 2

Cerius 2 provides an easy-to-use simulation and modeling environment, offering a broad range of scientific application modules. MSC has the selected Cerius 2 modules listed below. To access this software, please contact the MSC Consultants by sending e-mail to mscf-consulting@emsl.pnl.gov.

C2-Crystal Builder

C2-Surface Builder

C2-DMol3 Solid State

C2-DMol3 is a density functional theory (DFT) program with the unique ability to handle either molecular clusters or periodic systems. DMol3 allows you to understand the reactivity and properties of a broad range of systems, including organic molecules, organometallics, inorganic solids, and surfaces.

C2-CASTEP

CASTEP is a quantum mechanics module used to simulate the properties of solids, interfaces, and surfaces for a wide range of materials classes including ceramics, semiconductors, and metals. You can determine quantities such as geometric structure, energies, band-structures, and charge density.

AMBER - Assisted Model Building with Energy Refinement
(version 9)

"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. MSC has a site license agreement.