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. AMMP
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 MMTK
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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.
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. free chemistry software
OVITO - The Open Visualization Tool OVITO is a scientific visualization and analysis software for atomistic simulation data developed by Alexander Stukowski at Darmstadt University of Technology, Germany. The program is Open Source and freely available for all major platforms. An article about OVITO was published in the journal Modelling and Simulation in Materials Science and Engineering in 2010. Since then, OVITO has served in a growing number of computational materials science studies, helping to analyze, understand, and illustrate research results.
This is a list of computer programs that are predominantly used for molecular mechanics calculations. Y - Yes.I - Has interface. See also Notes and references List of software for molecular mechanics modeling
NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD - Scalable Molecular Dynamics
VMD - Visual Molecular Dynamics News and Announcements GPU-accelerated molecular visualization on petascale supercomputing platforms, UltraVis'13 Most cited since 2008: "GPU-Accelerated Molecular Modeling Coming of Age" Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters, Proc. XSCALE, 2013.
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.
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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 and allowing insight into molecular motion on an atomic scale.
CP2K is a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems. It provides a general framework for different methods such as e.g., density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials. CP2K is freely available under the GPL license. It is written in Fortran 95 and can be run efficiently in parallel. Strengths and limitations CP2K homepage
LAMMPS Molecular Dynamics Simulator lamp: a device that generates light, heat, or therapeutic radiation; something that illumines the mind or soul -- www.dictionary.com hover to animate -- input script physical analog (start at 3:25) & explanation LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. 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.