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]

votca

claimed by Max Planck Institute for Polymer Research

Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) is a package intended to reduce the amount of routine work when doing systematic coarse-graining of various systems. The core is written in C++. Iterative methods are implemented using bash + perl.

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]

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]

acpypi

Welcome to ACPYPI!A tool based on Python to use Antechamber to generate topologies for chemical compounds and to interface with others python applications like CCPN tools or ARIA. acpypi is pronounced as "ace + pipe". Topologies files to be generated so far: CNS/XPLOR, GROMACS ... [More] , CHARMM and AMBER. Latest version of ANTECHAMBER can be found in AmberTools 1.2. NB: Topologies generated by acpypi/Antechamber are based on General Amber Force Field (GAFF) and should be used only with compatible force fields like AMBER and its variants. Several flavours of AMBER FF are ported already for GROMACS (see ffAMBER) as well as for XPLOR/CNS (see xplor-nih) and CHARMM. Please, read ACPYPI Wiki pages for more information. It was inspired by:amb2gmx.pl by Eric Sorin, David Mobley and John Chod [Less]

xtcio

xtcio is a library for read and write xtc file. xtc file format come from gromacs, but the gromacs library is too huge. so I pick the xtcio from gromacs as an isolated library.

votca-ctp

claimed by Max Planck Institute for Polymer Research

Charge carrier dynamics in an organic semiconductor can often be described in terms of charge hopping between localized states. The hopping rates depend on electronic coupling elements, reorganization energies, and driving forces, which vary as a function of position and orientation of the ... [More] molecules. The exact evaluation of these contributions in a molecular assembly is computationally prohibitive. Various, often semi-empirical, approximations are employed instead. The purpose of the toolkit is to simplify the workflow for charge transport simulations, provide a uniform error-control for the methods, flexible platform for their development, and eventually allow in silico pre-screening of organic semiconductors for specific applications. [Less]

gridcount

gridcount is an analysis tool for Gromacs that creates 3D (number) densities from molecular dynamics trajectories. Typically, this is used to look at the density of water or ions near proteins or in channels. It provides tools to generate the 3D map in portable formats, 2D cylindrical averages and 1D linear averages ("density profiles")

g_count

g_count and g_flux are simple Gromacs tools that are primarily useful to characterize movement of water inside a cylindrical region. This can be the pore of an ion channel or a carbon nanotube. g_count returns statistics about how many atoms of a certain type (for instance, water oxygens) occupied ... [More] the region of interest. g_flux calculates the flux through a cylindrical region. g_flux is more sophisticated than g_count and gives more detailed information. Citation: O. Beckstein and M. S. P. Sansom, The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores, Phys. Biol. 1 (2004), 42–52. doi:10.1088/1478-3967/1/1/005 [Less]