This repository contains a Google Colab notebook designed for running high-performance Molecular Dynamics (MD) simulations using NAMD 3 with CUDA acceleration.
- End-to-End Pipeline: Handles Setup, System Configuration, Minimization, Equilibration, and Production.
- Automated Configuration: Dynamically generates NAMD
.conffiles based on user inputs. - Performance Optimized:
- Uses CUDA for GPU acceleration.
- Optimizes CPU affinity and core usage.
- Mitigates Google Drive I/O latency by writing logs locally.
- Google Drive Integration: Seamlessly mounts Drive for input files and automatic result backups.
- Upload to Drive: Place your
.pdb,.psf, and parameter files in a folder on Google Drive. - Open in Colab: Upload
NAMD3_Simulation.ipynbto Google Colab. - Configure: Set your file paths and simulation parameters in the "System Configuration" cell.
- Run: Execute the cells to perform the simulation.
- Google Colab (Free or Pro) with GPU runtime (T4 recommended).
- NAMD 3 (downloaded automatically by the notebook).
- Valid PDB/PSF system files.
Copyright (c) 2025 Dip Kumar Ghosh
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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