NexusMD

A Molecular Dynamics Simulation Package for Drug Discovery

Description

NexusMD is the next-gen molecular dynamics simulation software package to predict protein-ligand binding affinities in drug discovery. NexusMD is equipped with modern free energy methods, novel sampling algorithms, and GPU-accelerated parallelism for diverse scientific applications.
This repository provides a Python showcase (C++/CUDA backend source code available on request) of the NexusMD interface. It contains a minimal test setup and examples so users can explore how NexusMD simulations are configured and executed.

Table of Contents

• Description
• Architecture
• Getting Started
  • Dependencies
  • Installation (Published Version)
• Expected Output
• Current Status
• Version History
• License

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Architecture

NexusMD is organized in simple layers so users configure simulations in Python while heavy computation runs in native backends. At a high level:

• Frontend – A Python API loads inputs, sets options, and launches a run.
• Orchestration – Chooses CPU or GPU execution and prepares the data required by the backend.
• Core Engine – Advances the simulation step-by-step, coordinating force evaluation, integration, constraints, and controllers.
• Data & I/O – Reads common input formats (e.g., PDB/XML), manages necessary transfers between host and accelerator, and writes coordinates/energies at user-defined intervals.
• Extensibility – New forces and analysis features can be added as plugins without changing the core workflow.

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Getting Started

Dependencies

• Python: Version 3.11

• Operating Systems:

  • Windows 10, 11
  • Linux (Tested on Ubuntu 20.04 or later)

• Execution via the source code:

  • For Windows: Visual Studio 2022
  • For Linux: GCC or Clang (latest version recommended)

• CUDA: Required for GPU Acceleration.

• Execution the published version: Anaconda

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Installation Instructions (Published Version)

Windows

1. Install Anaconda:

   • Download and install Anaconda from the official website.
   • Select the following Advanced Installation Options during installation:

2. Create a New Anaconda Environment:

   • Press Win + S and type Environment Variables.
   • Open the Anaconda Prompt.
   • Create a new environment with Python 3.11:

     conda create -n nexusMD_env python=3.11

   • Activate the environment:

     conda activate nexusMD_env

3. Install NexusMDMD library:

   • run the following command to install NexusMD 1.2.0 MD software package:

     pip install -i https://test.pypi.org/simple/ NexusMD

4. Prepare the Folder:

   • Create a folder (preferebly on your Desktop for easy navigation on Anaconda Prompt) to contain all necessary files (available in the test folder (NexusMD github repository)):
     • dhfr_ecoli_protein.pdb: The PDB file for the system.
     • system_dhfr_ecoli_protein.xml: The system XML configuration file.
     • state_dhfr_ecoli_protein.xml: The state XML configuration file.
     • NexusMDTest.py: Test script for NexusMD.
   • Copy these files into the folder.

5. Adjust Options in NexusMDTest.py:

   • Open NexusMDTest.py in any text editor or IDE. A straightforward option's Notepad++
   • Adjust any of the following parameters inside the NexusMDTest.py to enable or disable their inclusion during the MD simulation.

        conf = cfg()
        conf.systemXml = "system_dhfr_ecoli_protein.xml"
        conf.stateXml  = "state_dhfr_ecoli_protein.xml"
        conf.pdbInput  = "dhfr_ecoli_protein.pdb"
        conf.pdbOutput = "output_SimRun_dhfr_ecoli_protein.pdb"
        
        conf.useCuda     = True   
        conf.steps       = 100
        conf.reportEvery = 10
        
        conf.forceHarmonicAngle   = True
        conf.forceHarmonicBond    = True
        conf.forcePeriodicTorsion = True
        conf.forceNonbonded       = True
        
        conf.enableThermostat(300.0, 10.0) 
        conf.enableBarostat(1.0, 200)     
        
        conf.rigidWater    = True
        conf.hcovalentBond = True

6. Run NexusMDTest.py:

   • Navigate to the folder in the Anaconda Prompt make sure nexusMD_env environment is activated.
   • Run the test script:

     python NexusMDTest.py

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Key Notes

• Ensure the .pdb, .xml, and NexusMDTest.py files are all in the same folder for convenience.
• Adjust any parameters in the NexusMDTest.py file to match your use case (e.g., simulation parameters, desired forces, controllers, and constraints to enable, etc.).
• Output and results will depend on the configuration of the provided .xml and .pdb files.

Expected Output

Terminal Output

[NexusMD] run(): start
[md] CUDA              : ON
[md] Harmonic Bond     : ON
[md] Harmonic Angle    : ON
[md] Periodic Torsion  : ON
[md] Non-bonded        : ON
[md] Thermostat        : ON
         T = 300 K   Frequency = 10 1/ps
[md] Barostat          : ON
         P = 1 bar   every 200 steps
[md] Rigid water       : ON
[md] H-covalent shake  : ON
step: 0
step: 1
step: 2
step: 3
step: 4
step: 5
step: 6
step: 7
step: 8
step: 9
step: 10
[NexusMD] run(): done

Generated Files

• output_SimRun_dhfr_ecoli_protein.pdb – Final simulation output in PDB format.
• PVFReportoutput_SimRun_dhfr_ecoli_protein.pdb – Contains position, velocity, and force quantities.
• TotalEnergyoutput_SimRun_dhfr_ecoli_protein.pdb – Records kinetic, potential, and total energy values in kJ/mol.
• EnsembleReportoutput_SimRun_dhfr_ecoli_protein.pdb – Contains Kinetic Energy, Potential Energy, Temperature, Box Volume and Density quantities related to controllers performance.
• SettleReportoutput_SimRun_dhfr_ecoli_protein.pdb – Contains rigid water constraint performance .
• ShakeReportoutput_SimRun_dhfr_ecoli_protein.pdb – Contains hydrogen covalent bond constraint performance .

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Current Status

• Functional Python API with backends (CPU or CUDA).
• End-to-end simulation loop: forces → integration → constraints → controllers → reporting.
• Input parsing for PDB/XML and system initialization.
• Periodic boundary wrapping and analysis outputs.
• Constraints (rigid water; H-covalent bonds) and controllers (thermostat; barostat).
• Reporting of coordinates and energies/ensemble/constraints properties.
• Automated Cross-platform builds under active testing (Windows, Linux tested).
• Public API and file formats are experimental and may change between versions.

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Version History

• 1.0.0
  • Initial Release
• 1.2.0
  • Prototype Release

License

Nexus is licensed under the MIT License. See LICENSE for details.