Managed Projects
mdanalysis
Analyzed 1 day 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
Licenses:
gpl
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...
gridcount
G
Analyzed 1 day 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 1 day 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
alchemlyb
A
Analyzed about 20 hours ago
alchemlyb is makes alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack. It includes:
- Parsers for extracting raw data from output files of common molecular dynamics engines such as GROMACS, AMBER, or NAMD.
- Subsamplers for obtaining
Licenses:
No declared licenses