gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
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May 23, 2026 - Python
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gromacs
Here are 114 public repositories matching this topic...
OFFICIAL: AnteChamber PYthon Parser interfacE
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May 20, 2026 - Python
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
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May 20, 2026 - Python
Fully automated high-throughput MD pipeline
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Mar 11, 2026 - Python
a python package for the interfacial analysis of molecular simulations
python molecular-dynamics openmm scientific-computing data-analysis lammps charmm simulations molecular-simulations namd gromacs interfaces mdanalysis mdtraj willard-chandler interfacial-atoms sasa
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Jun 6, 2026 - Python
A project (and object) for storing, manipulating, and converting molecular mechanics data.
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Jun 2, 2026 - Python
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
python cli benchmark simulation molecular-dynamics computational-chemistry high-performance-computing namd gromacs
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Sep 5, 2024 - Python
Generate coarse-grained molecular dynamics models from atomistic trajectories.
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Nov 26, 2025 - Python
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
optimization molecular-dynamics optimization-tools gromacs coarse-grained coarse-graining molecular-modeling bonded-terms bonded-parameters swarm-cg cg-model
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Aug 19, 2024 - Python
Full automation of relative protein-ligand binding free energy calculations in GROMACS
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May 3, 2021 - Python
Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)
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Jul 17, 2024 - Python
To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories.
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Apr 15, 2025 - Python
Calculation of water/solvent partition coefficients with Gromacs.
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Oct 14, 2024 - Python
PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis
simulation hpc molecular-dynamics protein namd gromacs markov-state-model amber ims tsubame issp fugaku pacsmd
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Dec 14, 2025 - Python
NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.
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May 3, 2025 - Python
lindemann is a python package to calculate the Lindemann index of a lammps trajectory
chemistry analysis cheminformatics simulation molecular-dynamics lammps chemoinformatics gromacs ovito phase-transition lindemann md-simulation phase-transitions lindemann-index transition-phase lammps-trajectory temperature-ramps
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Jun 11, 2024 - Python
Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)
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Apr 27, 2026 - Python
User friendly molecular dynamics simulation combining Modeller, OpenMM and Google Colab: A complete guide
python cheminformatics simulation protein-structure protein gromacs mdanalysis mdtraj ligand colab-tutorial
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Jun 7, 2026 - Python
Molecular Dynamics Simulation of Alanine Dipeptide and Dihedral Angle Analysis
simulation molecular-dynamics alanine-dipeptide gromacs dihedral-angles mdanalysis ramachandran-plot
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Jan 2, 2024 - Python
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