untitled

Energy minimization software

Red - Costware Green - Freeware or Sharware

Site Name and Address

Brief Summary of Site

Amber
Amber (Mirror)
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. Though Amber is costware, it is very inexpensive.

Argus Program costs money but they have a Demo. Argus will allow molecule building, molecular mechanics, molecular dynamics, and quantum calculations.

Batch Man BatchMan runs under Windows (9x and NT) and is both a viewer and an interface to MOPAC and GAMESS.

GRASP GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties. The program does cost money but only $500..

GROMACS 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 have a lot of complicated bonded interactions.

Insight Makers of InsightII and other related programs. Full featured molecular modeling program at a substantial price.

INTERPROBE This is a general-purpose molecular modelling program which uses the graphics facilities of Silicon Graphics workstations for display of structures, and for molecular-mechanics and quantum-chemistry calculations. It is suited to calculations on both low- and high-molecular weight systems, and has many features incorporated for treating protein and enzyme structures. It is the cornerstone software to which many of the other programs are linked.

LAMMPS LAMMPS is a molecular MD code most suitable for modeling biological systems or polymers. It contains efficient long-range Coulombic solvers and a variety of force-fields.

McSym McSym is a program similar to NAB though directed at RNA rather than DNA.

MMTK The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations.

MODELLER MODELLER is used for homology or comparative modeling of protein three-dimensional structures

MOIL The MOIL modeling package to simulate structure, dynamics, and function of biological molecules at the atomic level of detail. Can handle problems which require long simulations and LES. Has windows graphic interface. Runs on common Unix ( IBM RS/6000 & SP 2, SGI, Sun, Dec), Linux, and Windows (NT & WIN98).

Moloc Moloc is a molecular modeling package designed with emphasis on high interactivity. Since 1986 it has been, and now continues to be developed in close collaboration with drug designers and crystallographers of the Roche Biostructural community.

MolPro MOLPRO is a complete system of ab initio programs for molecular electronic structure calculations. As distinct from other commonly used quantum chemistry packages, the emphasis is on
highly accurate computations, with extensive treatment of the electron correlation problem through the
multiconfiguration-reference CI, coupled cluster and associated methods

NAB NAB (Nucleic Acid Builder) is a computer language (specified through lex and yacc) that allows nucleic acid structures to be described in a hierarchical fashion, using a language similar to C or awk, but designed especially for the manipulation of nucleic acid structures.

NAMD NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.

NWChem NWChem is a suite of programs that includes quantum mechanical, MM, MD, and QM/MM into one package. It can be run under both serial and parallel modes and on Unix/linux/Mac platforms.

Q-Chem Ab initio quantum chemistry software program

QCPE Offers source code on a wide range of computational chemistry programs and very low prices. Major categories include MM3, NMR/ESR simulation, MOPAC and others

PlotAmber This is a program to pull out various pieces of information from the Amber md.out file and reformat them for a suitable plotting program such as xmgr (aka grace).

PMEMD PMEMD is a new version of the Amber module "Sander", and has been written with the major goal of improving performance in Particle Mesh Ewald molecular dynamics simulations and minimizations.

Sybyl/Unity Makers of Sybyl and Unity. General, commercial, and expensive molecular modeling program.

Tinker The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.

WebMO WebMO is a World Wide Web-based interface to computational chemistry packages.
WebMO is available for free and can be installed on nearly any unix or Linux system.

Computational Resources on the Web List like this one with lots of resources/links.

Site Name and Address	Brief Summary of Site
Amber Amber (Mirror)	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. Though Amber is costware, it is very inexpensive.
Argus	Program costs money but they have a Demo. Argus will allow molecule building, molecular mechanics, molecular dynamics, and quantum calculations.
Batch Man	BatchMan runs under Windows (9x and NT) and is both a viewer and an interface to MOPAC and GAMESS.
GRASP	GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties. The program does cost money but only $500..
GROMACS	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 have a lot of complicated bonded interactions.
Insight	Makers of InsightII and other related programs. Full featured molecular modeling program at a substantial price.
INTERPROBE	This is a general-purpose molecular modelling program which uses the graphics facilities of Silicon Graphics workstations for display of structures, and for molecular-mechanics and quantum-chemistry calculations. It is suited to calculations on both low- and high-molecular weight systems, and has many features incorporated for treating protein and enzyme structures. It is the cornerstone software to which many of the other programs are linked.
LAMMPS	LAMMPS is a molecular MD code most suitable for modeling biological systems or polymers. It contains efficient long-range Coulombic solvers and a variety of force-fields.
McSym	McSym is a program similar to NAB though directed at RNA rather than DNA.
MMTK	The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations.
MODELLER	MODELLER is used for homology or comparative modeling of protein three-dimensional structures
MOIL	The MOIL modeling package to simulate structure, dynamics, and function of biological molecules at the atomic level of detail. Can handle problems which require long simulations and LES. Has windows graphic interface. Runs on common Unix ( IBM RS/6000 & SP 2, SGI, Sun, Dec), Linux, and Windows (NT & WIN98).
Moloc	Moloc is a molecular modeling package designed with emphasis on high interactivity. Since 1986 it has been, and now continues to be developed in close collaboration with drug designers and crystallographers of the Roche Biostructural community.
MolPro	MOLPRO is a complete system of ab initio programs for molecular electronic structure calculations. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods
NAB	NAB (Nucleic Acid Builder) is a computer language (specified through lex and yacc) that allows nucleic acid structures to be described in a hierarchical fashion, using a language similar to C or awk, but designed especially for the manipulation of nucleic acid structures.
NAMD	NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.
NWChem	NWChem is a suite of programs that includes quantum mechanical, MM, MD, and QM/MM into one package. It can be run under both serial and parallel modes and on Unix/linux/Mac platforms.
Q-Chem	Ab initio quantum chemistry software program
QCPE	Offers source code on a wide range of computational chemistry programs and very low prices. Major categories include MM3, NMR/ESR simulation, MOPAC and others
PlotAmber	This is a program to pull out various pieces of information from the Amber md.out file and reformat them for a suitable plotting program such as xmgr (aka grace).
PMEMD	PMEMD is a new version of the Amber module "Sander", and has been written with the major goal of improving performance in Particle Mesh Ewald molecular dynamics simulations and minimizations.
Sybyl/Unity	Makers of Sybyl and Unity. General, commercial, and expensive molecular modeling program.
Tinker	The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.
WebMO	WebMO is a World Wide Web-based interface to computational chemistry packages. WebMO is available for free and can be installed on nearly any unix or Linux system.
Computational Resources on the Web	List like this one with lots of resources/links.