Search Results for "molecular"

http://loto.sourceforge.net/ hosts 4 projects of free software related to materials science and physics. They are loto, feram, compasses and xtalgrowth.

PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use...

Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.

This software has moved to http://www.poissonboltzmann.org/.

This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. ...

This project and all source code has moved to GitHub, see https://github.com/virtualcell

NX is a program for nonadiabatic molecular dynamics in the electronic excited states. It is based on the surface hooping approach.

...Straightforwad use of ANT.G include the computation of the zero-bias conductance (or, alternatively, the electrical current under an applied bias voltage) of a variety of nanoscale systems such as molecular bridges or simply metallic atomic contacts as those created with scanning tunneling microscope or break junction techniques. The use of ANT.G may also be naturally extended to the computation of scanning tunneling spectroscopy and the simulation of scanning tunneling and electrostatic force microscopy.

This program allows to perform a structural cluster analysis of atomic trajectories obtained, e.g., from molecular dynamics simulations. At variance with other approaches, it is possible to analyse also processes in solution, e.g., chemical reactions in liquid water, since the distance metric is based on a Permutation Invariant Vector (PIV) that is symmetric under exchange of identical atoms or molecules, including on the same footing both solute and solvent degrees of freedom. ...

is a molecular viewer & model builder for quantum chemistry programs. It has an interface with NWChem, CP2K and PC GAMESS/Firefly quantum programs. http://www.biomolecular-modeling.com/Products.html

SMMP (Simple Molecular Mechanics for Proteins) is a program library for protein simulations with an emphasis on advanced Monte Carlo algorithms. It includes various force fields to calculate the energy of a protein and protein-protein interactions.

BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.

Monte Carlo implementation for the "Mobile Charge Densities in Harmonic Oscillators" (MCDHO) Molecular Force Field for Numerical Simulations of Biological Systems