Projects

GROMACS

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] 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. [Less]

ESPResSo++

claimed by Max Planck Institute for Polymer Research

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 Soft Matter Simulation Software

claimed by Max Planck Institute for Polymer Research

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

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] It also allows for modularization and code re-use. In addition, commands, warnings and errors are logged to a file so that there exists a complete history of what has been done. [Less]

FreeON

claimed by Los Alamos National Lab

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] distributions and OS X. FreeON performs Hartree-Fock, pure Density Functional, and hybrid HF/DFT calculations (e.g. B3LYP) in a Cartesian-Gaussian LCAO basis. All algorithms are O(N) or O(N log N) for non-metallic systems. Periodic boundary conditions in 1, 2 and 3 dimensions have been implemented through the Lorentz field (Γ-point), and an internal coordinate geometry optimizer allows full (atom+cell) relaxation using analytic derivatives. Effective core potentials for energies and forces have been [Less]

mdanalysis

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] framework for complex analysis tasks. In addition, CHARMM-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out. Some time-critical routines are written in C or Cython and require a working C compiler. MDAnalysis comes with an expanding library of analysis functions such as RMSD-fitting or analysis of lipid membrane bilayers. [Less]

VMD pbctools

Plugin for the VMD molecular viewer that handles periodic boundary conditions.

debyer

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] scattering structure function, pair distribution function (PDF) and related functions (RDF, reduced PDF). It can also convert between a few file formats (XMOL xyz, AtomEye cfg, DL_POLY CONFIG, LAMMPS data file, PDB). Although the program can take a unit cell as input, there are more suitable programs to calculate a diffraction pattern of a perfect crystal. dbr_extendA tool to manipulate atomistic configuration file. Most useful for bicrystals. For example, it can extend the system, cut out a slab from the system, create a supercell or shift all the atoms under under PBC. In some of the tasks, like extending the system, local periodicity of the structure is determined first. dbr_bondsCalculates coordination number of atoms, distribution of bond lengths and angles between bonds. [Less]

LOOS

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.

aviewer

Python interface to raster3D and movie creation.