Application Index

Programs or software systems for performing molecular dynamics simulations.

This is a program for Molecular building, graphics, dynamics, optimization, with an interface to Quantum chemistry package PC GAMESS/Firefly.
View Application Entry for Ascalaph

RedMD is a free open source package for molecular dynamics simulations and normal mode analysis for coarse-grained models of proteins, nucleic acids and their complexes. Force fields are based on elastic network models and their extensions. The code is written in C and C++, parallelized and available for Linux.
View Application Entry for RedMD (Reduced Molecular Dynamics)

AMBER is a package of molecular simulation programs which includes source code and demos. It is available for commercial and can be used on Unix Workstations or Parallel supercomputers.
View Application Entry for AMBER (Assisted Model Building with Energy Refinement)

SDA permits Brownian dynamics simulations to be carried out and the rates of bimolecular diffusional association of 2 molecules, e.g. 2 proteins, to be computed given the atomic structure of the bound complex of the 2 molecules. Proteins are represented as rigid bodies with all-atom detail accuracy. The interaction between the molecules is given by an approximation to the Poisson-Boltzmann equation-derived electrostatic interaction. Association events are monitored by means of different criteria.
View Application Entry for SDA: Simulation of Diffusional Association of proteins

We are pleased to announce the release of ProtoMol v2.0: an open source, object-oriented, component-based framework for molecular dynamics (MD) simulations. It supports CHARMM 19 and 28a2 force fields and is able to read and write PDB, PSF, XYZ, DCD, and several common graphics formats. ProtoMol is designed for high flexibility, ease of extendibility and maintenance, and high performance and scalability demands. We use MPI to implement atom- and force-based decompositions in a manner nearly transparent to both end-users and developers. The use of fast electrostatic force evaluation algorithms like particle mesh Ewald (PME), an O(n log n) method, and multigrid summation (MG), an O(n) method, further improve performance. In addition, MG has superior scalability when running in a parallel environment. ProtoMol contains many novel MD and Monte Carlo (MC) based methods suitable for simulation in a variety of ensembles. For example, shadow hybrid Monte Carlo (SHMC) has been shown to scale system size and MD timestep by a factor of 10 or more over hybrid Monte Carlo (HMC). Multiscale simulations may take advantage of longer timesteps by coupling multiple time-stepping algorithms with advanced integrators. Using targeted Molly, we have achieved stable timesteps of 16fs for solvated proteins. In addition, ProtoMol has been designed to interact with VMD, a visualization engine developed at the University of Illinois, which is used for displaying large biomolecular systems and running simulations in 3-D. Highlights of ProtoMol v2.0: - Average 50% performance increase versus ProtoMol 1.8.3 - Additional integrators including Shadow Hyrid Monte Carlo (SHMC), an NPT method based upon the work of Maryna, Tobias, and Klein, and an MD implementation of the isomolar-semigrand ensemble for computing phase equilibrium of mixtures. - An updated interface for adding new forces, integrators, and output methods - Improved code organization utilizing design patterns We invite you to visit the ProtoMol home page, http://protomol.sourceforge.net, where C++ source code, documentation, and prebuilt binaries may be found. Operating systems natively supported include Linux, SunOS, Irix, HP-UX and Windows. For questions or comments, please feel free to contact the ProtoMol team at protomol@cse.nd.edu.
View Application Entry for PROTOMOL

MM3 is a commercial program that performs molecular mechanics calculations. It is available as a stand-alone application or within the SYBYL/Base interface.
View Application Entry for MM3

SYBYL/Base is a computational tool kit for molecular design and analysis. It requires a license and will run on SGI platforms operating under IRIX 6.5 and higher and on HP platforms operating under HP-UX 11.0.
View Application Entry for SYBYL/Base

Discovery Studio (DS) is a complete range of life science applications spanning scientific disciplines within a single unified platform. It enables scientists to capture, manage, analyze, and use biological and chemical data and information.
View Application Entry for Discovery Studio (DS)

The Dynamo module library has been developed for the simulation of molecular systems using hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials. Dynamo is not a program package but is a library of Fortran 90 modules that can be employed by those interested in writing their own programs for performing molecular simulations. The library supports a range of different types of molecular calculation including geometry optimizations, reaction-path determinations and molecular dynamics and Monte Carlo simulations.
View Application Entry for DYNAMO

AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. In addition to standard features, like numerically stable molecular dynamics, fast multipole method for including all atoms in the calculation of long range potentials and robust structural optimizers, it has a flexible choice of potentials and a simple yet powerful ability to manipulate molecules and analyze individual energy terms. One major advantage over many other programs is that it is easy to introduce non-standard polymer linkages, unusual ligands or non-standard residues. Adding missing hydrogen atoms and completing partial structures, which are difficult for many programs, are straightforward in AMMP.
View Application Entry for AMMP (A modern full-featured Molecular mechanics, dynamics and Modeling Program)

CHARMm is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations. CHARMm is both a force field engine and the force field itself. This is the academic version named "CHARMM". The commercial version is named "CHARMm" with small "m" instead of large "M". It can be used on Unix Workstations.
View Application Entry for CHARMm

GROMACS is a high performance Molecular Dynamics Program for Parallel Computers using a well optimized code and smart algorithms. It is reasonably well optimized for low memory usage. The most CPU-intensive routines are in Fortran, but C routines are also available. GROMACS runs on almost every platform (version 2.0 also runs on Windows95/NT using CygWin). Standard Makefiles are available for DEC, HP, Linux, SGI, Sun, SP2, Convex and some Cray machines. All Makefiles support multi-processor machines. It is free for non-commercial users.
View Application Entry for GROMACS (GROningen MAchine for Chemical Simulations)

Chem3D brings workstation quality molecular modeling and display to your desktop. Chem3D performs energy minimization and molecular dynamics, and sets up and controls electronic structure calculations with CS MOPAC, GAMESS, and Gaussian. View molecular surfaces, orbitals, electrostatic potentials, and more with Chem3D.
View Application Entry for Chem3D

Impact is a commercial molecular mechanics program specifically designed to handle large macromolecular simulations. The program effortlessly treats simulations on ligand-protein systems in solvation or in vacuo enabling the study of large systems in a timely manner.
View Application Entry for Impact

JMD is a Java applet which does molecular dynamics simulation. It was designed to help students understand collective Newtonian dynamics and statistical mechanics, as well as the Xebec Studio research on applying the Java technologies to molecular simulation.
View Application Entry for JMD (Java Molecular Dynamics)

EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation; even Windows95/NT PCs (with a GNU-C compiler) can be used. The energy function employed partially derives from the one used in the program X-PLOR of A. Brünger. EGO can read X-PLOR pdb, psf, and parameter files and EGO output files can be converted to X-PLOR DCD/crd files and read back into X-PLOR for further analysis of the resulting trajectories. EGO was developed for the simulation of large molecular systems on parallel computers (under PVM, MPI or PARIX). EGO uses a multiple time step algorithm combined with a structure adapted fast multipole method for the description of long range electrostatics. The method has been demonstrated to scale linearly with the number of atoms in the range of about 40,000 atoms.
View Application Entry for EGO

Ghemical is a Computational chemistry software package with GUIs for both GLUT and GTK+, and some nice 3D-visualization tools. It can do "all atoms" molecular mechanics and dynamics, although the current parameter set is very limited. It is written in C++, and hopefully offers a good framework for a generic freeware molecular modeling tool.
View Application Entry for Ghemical

The UHBD (University of Houston Brownian Dynamics) program is capable of solving the linearized and non-linear Poisson-Boltzmann equation using a finite-difference method. In addition, the program can be used to perform Brownian dynamics calculations for steady and non-steady state rate constants of encounter of a substrate/inhibitor with a target (enzyme). The UHBD code can also be used to perform stochastic dynamics calculations or molecular mechanics energy minimizations using the Poisson-Boltzmann and/or other molecular mechanics forces. The program also has the capability to compute electrostatic free energies of binding of two molecules and can include the non-electrostatic surface area changes and how that affects the energy.
View Application Entry for UHBD (University of Houston Brownian Dynamics)

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. MMTK is developed in and around Python, a high-level object-oriented general-purpose programming language. In fact, MMTK consists of nothing more than a collection of Python modules, most of which written in Python itself, with only a small time-critical part (e.g. energy evaluation) written in C. MMTK applications are Python programs that make use of these modules. Python was chosen because it allows rapid code development and testing, while providing a very convenient C interface for dealing with time-critical calculations. MMTK is based on an object-oriented model of molecular systems. A system is made up of atoms, molecules, and complexes, all of which are defined in MMTKs chemical database. A molecule, for example, is defined in terms of atoms, functional groups, bonds, force field parameters, etc. It is possible to introduce specialized versions of these objects; for example, MMTK has special support for proteins, which are basically chemical complexes, but can be handled in terms of peptide chains, residues, sidechains etc.
View Application Entry for MMTK

Mindy is a very simple, serial molecular dynamics program derived from NAMD source code. It currently uses xplor parameter and structure files. The program is written in very straightforward C++.
View Application Entry for Mindy

HINT! is a novel empirical molecular modeling system with new methods for de novo drug design and protein or nucleic acid structural analysis.
View Application Entry for HINT! (Hydropathic INTeractions)

Moldy is a general-purpose molecular dynamics simulation program. It is sufficiently flexible that it ought to be useful for a wide range of simulation calculations of atomic, ionic and molecular systems. The program is highly portable and has been optimised for both vector supercomputers (cray and convex), but also runs fast on modern unix workstations and even PCs.
View Application Entry for Moldy

DL_POLY is a parallel molecular dynamics simulation package.
View Application Entry for DL_POLY

MOIL is a free modeling package for simulating structure, dynamics, and function of biological molecules at the atomic level of detail. MOIL is available on the following platforms: IBM RS/6000 and SP, Windows NT and WIN98, PC linux, SGI, SUN and DEC.
View Application Entry for MOIL

MidasPlus is an advanced molecular modeling system developed in order to display and manipulate macromolecules such as proteins and nucleic acids. MidasPlus is supported on Silicon Graphics workstations, Digitial Equipment Alpha AXP workstations, and NeXT Computer workstations. Binaries for IBM RS/6000 and Linux workstations are also currently provided but these are not supported. For non-profit institutions and government agencies the cost of a MidasPlus license is $350.
View Application Entry for MidasPlus

Quanta provides a powerful and comprehensive modeling environment for 2D and 3D modeling, simulation, and analysis of biological macromolecules and small organics. Functionality includes structural and similarity analysis tools, cluster analysis, and flexible fitting. Advanced and customizable graphics display assists understanding of even the most complex molecular systems. Simulation and analysis results are presented as clear plots and graphs. With access to all standard file formats, and interfaces to CHARMm, MODELER, and multiple third party quantum and molecular mechanics (QM&MM) codes, QUANTA offers a complete solution for visualization and investigation of molecules in the life sciences. QUANTA runs on Silicon Graphics UNIX workstations and servers. The CHARMm simulation engine also runs on some IBM and Cray systems.
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SIgMA is a system of programs and data files for doing Energy minimization, Free Molecular dynamics, Constrained and restrained molecular dynamics and Molecular dynamics with free-energy methods.
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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.
View Application Entry for NAMD

The TINKER molecular modeling software is a free complete and general package for molecular mechanics and dynamics, with some special features for polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER-95, CHARMM22, MM2(1991), MM3(2000), OPLS-AA and OPLS-UA. Parameter sets for other standard force fields such as CHARMM27, ENCAD, MMFF and UFF are under consideration. In addition, we are actively developing our own TINKER force field based upon polarizable atomic multipole electrostatics. It can be used on Unix or Windows 95/98/2000/NT or Power Macintosh machines.
View Application Entry for TINKER

GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. It is free for academic users and is available for unix machines.
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MacroModel is a commercial molecular modeling software package allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations. It is available for Silicon Graphics or IBM workstations.
View Application Entry for MacroModel

X-PLOR is a commercial software for macromolecular simulation. It is used for studying the conformational space of macromolecules restrained to regions allowed by combinations of empirical energy functions and experimental data. It is available for unix workstations.
View Application Entry for X-PLOR

Cerius2 is a commercial multimodule software package that are capable of doing a wide variety of computations related to stuctural biology, chemistry, material science and physics from structural visualization, ligand docking, molecular simulation to quantum chemistry calculation. It is available for SGI IRIX 6.x and IBM AIX 4.x workstations and servers.
View Application Entry for Cerius2

Insight II is a commercial 3D graphical environment for molecular modeling. Its powerful user interface enables the seamless flow of data between a wide range of scientific applications. The Insight II environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences. It is available for Silicon Graphics or IBM RISC system/6000 workstations.
View Application Entry for Insight II