MultiScaleDPD

This repository contains the source code accompanying the paper: "Construction of Multiscale Dissipative Particle Dynamics (DPD) Models from Other Coarse-Grained Models".

And the (PENDING) paper: "Coarse-Grained Dissipative Particle Dynamics (DPD) Simulation of Cytochrome c Facilitated Binding Between Lipid Bilayers and Citrate-Coated Gold Nanoparticles"

Overview

MultiScaleDPD facilitates the construction of multiscale DPD models derived from existing coarse-grained models, enabling simulations in LAMMPS.

Features

• Model Conversion: Transform MARTINI models into DPD-compatible formats.
• LAMMPS Integration: Generate input files for seamless execution in LAMMPS.
• Customization: Support for advanced configurations, including the incorporation of additional molecular components like heme groups.
• Improved DPD Interactions: Incorporates enhanced pair interaction potentials for DPD simulations using pair_dpd.cpp.

Getting Started

Prerequisites

• Software:
  • CHARMM-GUI
  • LAMMPS
  • NumPy

Installation

1. Clone the Repository:

   git clone https://github.com/rxhernandez/MultiScaleDPD.git

2. Navigate to the Directory:

   cd MultiScaleDPD

3. Install Dependencies:

   pip install numpy

Building LAMMPS

To use the improved pair_dpd.cpp file, you need to build LAMMPS with the appropriate modifications:

1. Obtain LAMMPS Source Code:

   • Clone the LAMMPS repository:

   git clone https://github.com/lammps/lammps.git
   cd lammps

2. Replace pair_dpd.cpp:

   • Copy the provided pair_dpd.cpp file into the src/DPD-BASIC directory of the LAMMPS source code:

   cp /path/to/MultiScaleDPD/pair_dpd.cpp src/DPD-BASIC/

3. Build LAMMPS:

   • Follow the official instructions to compile LAMMPS with your desired settings: Build LAMMPS

Usage

1. Build a MARTINI Model:

   • Utilize CHARMM-GUI with the MARTINI22 force field to construct your protein model.
   • Obtain the following files from the output:
     • step3_charmm2gmx.pdb (structure file)
     • PROA_P.itp (MARTINI force field file)

2. Prepare Files:

   • Place step3_charmm2gmx.pdb and PROA_P.itp in the same directory as lib.py and convert.py.

3. Modify convert.py:

   • Open convert.py and step3_charmm2gmx.pdb in a text editor.
   • Adjust line numbers in convert.py to correspond with step3_charmm2gmx.pdb.

4. Run Conversion Script:

   python convert.py

5. Execute LAMMPS Simulations:

   • Utilize equilibration.lmps and production.lmps as input files for LAMMPS.
   • Run the equilibration phase first, followed by the production phase.

6. Advanced Usage:

   • Refer to example2 for incorporating additional components, such as heme groups.
   • Ensure LAMMPS includes bug fixes up to July 2022.

Citation

If you utilize this codebase or database, please cite:

Wang, Y; Hernandez R.; ACS Omega 9, 17667 (2024). [https://doi.org/10.1021/acsomega.4c01868]

Acknowledgment

This work was supported by the National Science Foundation under Grant No. CHE-2001611, the NSF 884 Center for Sustainable Nanotechnology (CSN). The CSN is 885 part of the Centers for Chemical Innovation Program.

License

MultiScaleDPD code and databases are distributed under terms of the MIT License.