AMMP. 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. It is written in C and has been ported to many different computers. The source code is available under the GNU "copyleft" so that it is easy to follow exactly what the program is doing. MMTK. Document Actions 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.
The three most common usage patterns of MMTK are Writing Python scripts that make use of MMTK functions for standard simulation and modelling applications. This is similar to using other simulation packages with a scripting language (i.e. MMTK is developed in and around Python, a high-level object-oriented general-purpose programming language.
MMTK is based on an object-oriented model of molecular systems. MMTK's functionality includes Compared to standard modelling code written in Fortran, MMTK is much easier to understand, extend, and modify. The VASP. The DL_POLY Molecular Simulation Package. Skip navigation STFC Home > Computational Science and Engineering Department Home > Research and Development > Computational Chemistry > Software > DL_POLY > The DL_POLY Molecular Simulation Package CSE Home About us Careers in CSE, how to contact us, where to find us... Support and services Support and services Research and Development Advanced Research Computing Atomic and Molecular Physics Band Theory CCP4 Group Computational Biology Computational Chemistry Software ChemShell Projects Reports Computational Engineering Computational Materials Science Numerical Analysis Software Engineering Advanced Research Computing-Visualization CECAM at Daresbury Instruct Computational Centre for Integrated Structural Biology Online Resources Online Resources Publications Publications News and events News and events The DL_POLY Molecular Simulation Package Latest release: DL_POLY_4.05.1 in September 2013Upcoming events: General Information For more information, suggestions and feedback on the DL_POLY_4 Software & Licensing.
Linux and Chemistry. Great Free and Open Source Molecular Modeling Software List. Scientists have always been looking for Molecular Modeling software, which enables them to view structure of molecules in 2D and 3D space, rotate them as they wish, unders tand molecular patterns, DNA/RNA structures etc. These are highly focused/specialized software with lots of software development costs involved from scientific research companies. Interestingly, there are quite a few Open Source tools that can help one understand the Molecule details, perform molecule modeling etc. This is really encouraging for those who admire and support such open software tools. Please support them if you like! Recommended Reading: Gabedit Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, PCGamess and Q-Chem.
Jmol Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules and much more. PyMol A Virus Visualization QuteMol RasMol Sirius Molekel. Free chemistry software. Jmol Jmol: an open-source Java viewer for chemical structures in 3D wxDragon wxDragon is a visualization program for Gaussian, VASP, ADF, Turbomole, Gamess, WIEN2K, Siesta, ... Mercury Mercury offers a comprehensive range of tools for structure visualisation and the exploration of crystal packing. Gabedit Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, PCGamess and Q-Chem. Avogadro Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
ArgusLab A molecular modeling, graphics, and drug design program VMD is a very powerful molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. OVITO - The Open Visualization Tool. List of software for molecular mechanics modeling. This is a list of computer programs that are predominantly used for molecular mechanics calculations. Y - Yes.I - Has interface. See also[edit] Notes and references[edit] Jump up ^ M.
J. External links[edit] Packmol.
NAMD - Scalable Molecular Dynamics. VMD - Visual Molecular Dynamics. Gromacs. Table of contents No headers 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, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition: GROMACS provides extremely high performance compared to all other programs.
A podcast of an interview with David van der Spoel about the past, present and future of GROMACS can be found here. Computational Materials Science - NCSU Department of Materials Science and Engineering. Molecular dynamics. Molecular dynamics. Because molecular systems consist of a vast number of particles, it is impossible to find the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in numerical integration that can be minimized with proper selection of algorithms and parameters, but not eliminated entirely. For systems which obey the ergodic hypothesis, the evolution of a single molecular dynamics simulation may be used to determine macroscopic thermodynamic properties of the system: the time averages of an ergodic system correspond to microcanonical ensemble averages. MD has also been termed "statistical mechanics by numbers" and "Laplace's vision of Newtonian mechanics" of predicting the future by animating nature's forces[3][4] and allowing insight into molecular motion on an atomic scale.
History[edit] Areas of application and limitations[edit] and velocities . And. CP2K homepage. ABINIT. LAMMPS Molecular Dynamics Simulator. LAMMPS-ICMS - Homepage of Axel Kohlmeyer. This is an experimental version of LAMMPS with additional features made available for testing before they will be submitted for inclusion into the official LAMMPS tree. The source code is based on the developer svn mirror and kept up-to-date as much as possible. Most of the time, all changes from the upstream repository are integrated immediately, sometimes - when additional development work is needed to adapt the additional code in LAMMPS-ICMS to the changes in the official LAMMPS version - the tree may be lagging behind for a while. Don't hesitate to contact me, if you need some specific feature to be merged in. March 2014 Update: Development on LAMMPS-ICMS is still mainly in bugfix-and-performance-enhancements mode. Known Issues: Using /omp pair styles as part of a hybrid style currently can yield wrong per atom pressure and per atom energies, if there are more threads than atoms on any MPI task.
Last Merge of LAMMPS-ICMS code to Upstream LAMMPS: Version 23 Nov 2013 LAMMPS-ICMS Features.