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GROMACS
Analyzed about 21 hours ago
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
Licenses:
lgpl21
votca
Analyzed 1 day ago
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.
Licenses:
apache_2
mdanalysis
Analyzed about 7 hours ago
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
GromacsWrapper
No analysis available
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. It
Mostly written in language not available
Licenses:
gpl3_or_l...
local_pressure_gromacs
L
Analyzed about 8 hours ago
Branch of gromacs implementing local pressure tensor computations
Licenses:
No declared licenses
gridcount
G
Analyzed about 1 hour ago
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
Analyzed about 2 hours ago
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
votca-ctp
Claimed by Max Planck Institute for Po... Analyzed about 11 hours ago
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
Licenses:
apache_2