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GROMACS engine support to a3fe #76

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GROMACS engine support to a3fe #76

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@Roy-Haolin-Du Roy-Haolin-Du commented Dec 8, 2025

Description

Adds GROMACS engine support to a3fe, enabling ABFE using GROMACS alongside existing SOMD support.

Key Changes

  • Configuration: New GromacsConfig class for MDP parameter management
  • Simulation: GROMACS runner with SLURM job submission support
  • Analysis: MBAR, RMSD, and gradient processing for GROMACS output
  • File Processing: Utilities for reading .xvg files and processing trajectories

Todos

  • GROMACS configuration system
  • Simulation execution and job submission
  • Analysis module integration
  • Test coverage

Status

  • Ready to go

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