Search Packages

gmx-clusterbyfeatures

Features Based Conformational Clustering of Molecular Dynamics trajectories.

gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

gmx-mmpbsa

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

longbow

Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.

gromorg

Simple Gromacs python wrapper

swarm-cg

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

mdbenchmark

Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

pytim

a python package for the interfacial analysis of molecular simulations

mdpow

Calculation of water/solvent partition coefficients with Gromacs.

porems

Pore generator for molecular simulations.

dnamd

To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories

streamd

Streamd Python module to facilitate molecular dynamics

lindemann

lindemann is a python package to calculate the Lindemann index of a lammps trajectory

pycgtool

Generate coarse-grained molecular dynamics models from atomistic trajectories.

nmrformd

Calculate dipolar NMR relaxation time from molecular dynamics trajectory file

gmxpy

Wrapping GROMACS by python script for me

jlhpy

Contains input files and workflows underlying J. L. Hörmann, C. (刘宸旭) Liu, Y. (孟永钢) Meng, and L. Pastewka, “Molecular simulations of sliding on SDS surfactant films,” The Journal of Chemical Physics, vol. 158, no. 24, p. 244703, Jun. 2023, doi: 10.1063/5.0153397. as well as an installable Python package jlhpy.

fretlabel

Nucleic acid fluorescence labeling for all-atom MD simulations