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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 ... [More]
ESPResSo++ is a highy versatile, parallelized, scientific simulation software for coarse-grained simulations of atomic and molecular systems. ESPResSo++ is the descendant of the ESPResSo simulation software. It is implemented in C++ and controlled via Python.
ESPResSo is a highly versatile software package for scientific simulations and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research, with emphasis on charged systems.
GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts. This is generally superior to shell scripts because of python’s better error handling and superior data structures. ... [More]
FreeON is an experimental, open source (GPL) suite of programs for linear scaling quantum chemistry. It is highly modular, and has been written from scratch for N-scaling SCF theory in Fortran95 and C. Platform independent I/O is supported with HDF5. FreeON should compile with most modern Linux ... [More]
MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, NAMD, LAMMPS, or Gromacs. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively fast ... [More]
You can find here a collection of C/C++ tools that work with atomistic models. debyerThe program takes as an input a file with positions of all the atoms in the virtual sample (up to tens of millions of atoms, perhaps even more) and can output x-ray and neutron powder diffraction pattern, total ... [More]
LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods.