Category: Molecular Simulation

Molecular simulation programs used to study the dynamic and thermodynamic behavior of molecular system.

Amber

Description

AMBER:Assisted Model Building with Energy Refinement

AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

Home Page

http://amber.scripps.edu

Tutorial

Amber Tutorials

Documentation

Remote online documentation can be found on the Amber 7 Manuals and Amber 8 Manuals

Setting Up Your Environment

There are several versions of Amber: serial version, shared-memory parallel (multiprocessor) version (MP) and parallel version that uses MPI message-passing library. The MP version is only available on multi-processor SGI computers. The MPI version is available on SGI Origin computers.
Note: Although serial and parallel versions share most of the code base, there are significant differences. In some cases, parallel version may not produce the same results as the serial version. The results for any new problem obtained with a parallel version should be carefully checked against the serial version. The two parallel verions, MP and MPI, are also significantly different from each other. The MP versions supports a richer set of features, but MPI version may provide better performance in certain cases. The MP version is generally more reliable. You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated files. To do this, enter the following commands:
To initialize serial version 8 of Amber: module add amber/amber8
To initialize serial version 7 of Amber: module add amber/amber7
Only Sander and Gibbs are parallelized in amber.
To access serial sander and gibbs, use command "sander_ser" and "gibbs_ser".
To acess parallel sander and gibbs, use the command "sander_par" and "gibbs_par".
If you access this package on a regular basis, you can add the above lines to your ~/.cshrc file so that your environment will be initialized for Amber every time you log in.

Version: v7.0, v8.0
Labs: IBM SP, IBM regatta, Scientific Development and Visualization Lab, Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all UNIX workstations and servers
Categories: Molecular Modeling, Chemistry, NMR, Molecular Simulation

Jaguar 5

Description (taken from Jaguar homepage)

Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory. Jaguar's speed and power make it possible to study larger systems than ever before, or to study many more systems than previously possible, within a reasonable timeframe.

Jaguar now uses Maestro as a common graphical user interface. To find out more, please refer to Maestro software documentation

Documentation

http://www.schrodinger.com

Running

First load the Jaguar module
To launch the Jaguar graphical interface type:
To run Jaguar from the command line type:
the input filename needs the suffix *.in; for example, filename.in.

To submit Jaguar jobs to the queue please use the qjag script,

qjag [options] filename

[options]: 

  -h prints the help menu
  -e [never] email notification (options: end or never)
  -m [300mb] amount of memory (append with mb of gb; ###mb)
  -r [yes] submit the job? (options: yes or no)
  -t [5:00:00] the amount of wall clock time (format: hh:mm:ss)

When using the qjag script the filename suffix .in is not required.

Sample files

/usr/local/schrodinger/jaguar-v55011/samples

Version:5
Labs:Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI workstations
Categories: Chemistry, Molecular Simulation

MacroModel

MacroModel consists of several programs. Macromodel is one of the programs and is used to build, manipulate and display organic chemical structures. BatchMin is a non-interactive, batch-mode modeling program used to minimize the energy of one structure or a series of structures, to eliminate duplicate conformations and to conduct molecular dynamics simulations with calculation of average enthalpy. BatchMin is called by MacroModel and is its use is usually transparent. However, for advanced applications, an understanding of BatchMin may be necessary. MacroModel can read files in its own format and PDB files. Manuals for MacroModel and BatchMin are in the Technical Documentation Center. Online help from within MacroModel is also available. Further information about Macromodel may be obtained from the MacroModel Home Page

MacroModel now uses Maestro as a common graphical user interface. To find out more, please refer to Maestro software documentation.

Version: 8.1
Labs: Scientific Development and Visualization Lab, Basic Sciences Computing Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all SGI workstations
Categories: Chemistry, Molecular Modeling, X-ray Crystallography, Molecular Simulation

Maestro

The Maestro is graphical user interface (GUI) for a series of products from Schrodinger. For brief description of current licensed schrodinger software, please see below for further information

The following modules are available to MSI researchers:

Package Concurrent Users Description (from the Schrodinger, Inc. web site)
Maestro unlimited The Maestro is graphical user interface (GUI) for a series of products from Schrodinger such as impact, jaguar, mac romodel and minta. It allows users to interact both graphically and textually and allows the user to create and di splay complex chemical structures, start and monitor a variety of calculations, and analyze structures and results of calculations.

Qsite 22
QSite is a new mixed mode QM/MM program for highly accurate energy calculations of protein-ligand intera ctions in the active site. The program is specifically designed for proteins and allows a number of diff erent QM/MM boundaries for residues in the active site. QSite uses the power and speed of Jaguar to perf orm the quantum mechanical part of the calculations and OPLS-AA to perform the molecular mechanical part of the calculations.

Jaguar 22
Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory. Jaguar's speed and power make it possible to study larger systems than ever before, or to study many more systems than previously possible, within a reasonable timeframe.

Macromodel 44
MacroModel is a general-purpose package for performing molecular mechanics for small and medium-sized organic molecules in both gas and solution phases. MacroModel has powerful utilities for exploring proteins and protein-ligand complexes. The program offers state-of-the art techniques for evaluating energy, sampling conformations, and accounting for solvation.

Minta 32
Minta allows for efficient calculation of free energy of molecular complexes as well as for individual ligands. Based on conformational analysis, Minta provides direct evaluation of free energies without recourse to long simulations or computational alchemy.

Package	Concurrent Users	Description (from the Schrodinger, Inc. web site)
Maestro	unlimited	The Maestro is graphical user interface (GUI) for a series of products from Schrodinger such as impact, jaguar, mac romodel and minta. It allows users to interact both graphically and textually and allows the user to create and di splay complex chemical structures, start and monitor a variety of calculations, and analyze structures and results of calculations.
Qsite	22	QSite is a new mixed mode QM/MM program for highly accurate energy calculations of protein-ligand intera ctions in the active site. The program is specifically designed for proteins and allows a number of diff erent QM/MM boundaries for residues in the active site. QSite uses the power and speed of Jaguar to perf orm the quantum mechanical part of the calculations and OPLS-AA to perform the molecular mechanical part of the calculations.
Jaguar	22	Jaguar was designed to increase the speed of ab initio calculations in order to accelerate basic and applied research projects and to enable calculations at a higher level of theory. Jaguar's speed and power make it possible to study larger systems than ever before, or to study many more systems than previously possible, within a reasonable timeframe.
Macromodel	44	MacroModel is a general-purpose package for performing molecular mechanics for small and medium-sized organic molecules in both gas and solution phases. MacroModel has powerful utilities for exploring proteins and protein-ligand complexes. The program offers state-of-the art techniques for evaluating energy, sampling conformations, and accounting for solvation.
Minta	32	Minta allows for efficient calculation of free energy of molecular complexes as well as for individual ligands. Based on conformational analysis, Minta provides direct evaluation of free energies without recourse to long simulations or computational alchemy.

For more information, please visit
http://www.schrodinger.com.

To initialize serial 2004 release of Maestro:

module add schrodinger/2004

To initialize serial 2005 release of Maestro:

module add schrodinger/2005

Labs:Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory, Basic Sciences Computing Lab
System(s): all SGI and linux workstations
Categories:Chemistry, Molecular Modeling, X-ray Crystallography, Molecular Simulation

Material Studio

MS Modeling is Materials Studio's modeling and simulation product suite, and is designed for structural and computational researchers in chemicals and materials R&D who need to perform expert-level modeling and simulations tasks in an easy to learn yet powerful environment. It provides flexible and validated tools for the study of materials at various length and time scales.

The following modules are available to MSI researchers:

Package Concurrent Users Description (from the Accelrys, Inc. web site)
MS Visualizer 2 MS Visulaizer - the core MS Modeling product, provides all of the tools that are required to construct graphical models of molecules, crystalline materials, and polymers. Additionally, the Visualizer lets you view and analyze these models and provides the software infrastructure and analysis tools to support the full range of Materials Studio products.

Amorphous Cell 1
Model construction and property prediction for amorphous materials particularly polymers.

Compass 1
A powerful molecular mechanics force field supporting simulations of solid materials.

Discover 1
molecular mechanics and dynamics methods for structure and property prediction.

Dmol 1
DMol3 - a unique density functional theory quantum mechanical code for gas phase, solvent, and solid state simulations.

Forcite 1
An advanced classical molecular mechanics tool, which allows fast energy calculations and reliable geometry optimization of molecules and periodic systems.

Polymorph Predictor 1 Polymorph Predictor - for the prediction of potential polymorphs of a given compound directly from the molecular structure.

Reflex 1 Reflex - powder diffraction simulation enhanced with indexing and refinement capabilities.

X-Cell 1 X-Cell - a novel and robust indexing program for medium- to high-quality powder diffraction data obtained from X-ray, neutron, and electron radiation sources.

For more information, see
http://www.accelrys.com/mstudio/ms_modeling.

For online documentation, see
http://www.accelrys.com/doc.

Package	Concurrent Users	Description (from the Accelrys, Inc. web site)
MS Visualizer	2	MS Visulaizer - the core MS Modeling product, provides all of the tools that are required to construct graphical models of molecules, crystalline materials, and polymers. Additionally, the Visualizer lets you view and analyze these models and provides the software infrastructure and analysis tools to support the full range of Materials Studio products.
Amorphous Cell	1	Model construction and property prediction for amorphous materials particularly polymers.
Compass	1	A powerful molecular mechanics force field supporting simulations of solid materials.
Discover	1	molecular mechanics and dynamics methods for structure and property prediction.
Dmol	1	DMol3 - a unique density functional theory quantum mechanical code for gas phase, solvent, and solid state simulations.
Forcite	1	An advanced classical molecular mechanics tool, which allows fast energy calculations and reliable geometry optimization of molecules and periodic systems.
Polymorph Predictor	1	Polymorph Predictor - for the prediction of potential polymorphs of a given compound directly from the molecular structure.
Reflex	1	Reflex - powder diffraction simulation enhanced with indexing and refinement capabilities.
X-Cell	1	X-Cell - a novel and robust indexing program for medium- to high-quality powder diffraction data obtained from X-ray, neutron, and electron radiation sources.

Version:3.0
Labs: Scientific Development and Visualization Lab, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): all PC's at VWL and sdvlapp1 at SDVL
Categories: Chemistry, Molecular Modeling, X-ray Crystallography, Molecular Simulation

NAMD

VMD - Visual Molecular Dynamics

NAMD is a molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. For more information, see NAMD home page.

Version: 2.3
Labs: Basic Sciences Computing Lab, Origin, IBM SP, Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory
System(s): Origin 2000, Origin 3000, IBM SP, SUN workstations at VWL
Categories: Molecular Modeling, Molecular Simulation