Effortlessly Prepare Coarse-Grained Models for GROMACS Simulations

Coarse-grained (CG) molecular dynamics simulations are a powerful tool to simplify molecular models and accelerate simulations. However, converting an atomistic structure into a reliable CG model with matching topology files can be daunting. What if you could streamline this process using a tool that ensures accuracy and efficiency? That’s exactly where SAMSON’s Martinize2 extension comes into play.

In this blog post, let’s explore how to create MARTINI CG models from atomistic structures, complete with GROMACS-compatible topology files, all within SAMSON.

The Challenge: Simplifying Complex Molecular Systems

Creating CG models manually involves approximating groups of atoms as beads, configuring topology files, and ensuring proper restraints for stability in simulations. Not only is this time-intensive, but inconsistencies can lead to unreliable results. A streamlined workflow provided by the Martinize2 SAMSON Extension enhances reliability while saving time.

Simplify Coarse-Graining: A Step-by-Step Approach

Here’s how you can easily convert an atomistic structure into a MARTINI CG model using Martinize2 in SAMSON:

  1. Load the Atomistic Structure: Start by importing your atomistic system into SAMSON. Use the Home > Fetch option to quickly download PDB files from RCSB PDB, or upload your custom structure. For example, you can work with the Ubiquitin protein (1UBQ).

  2. Prepare the Protein: Clean up your structure by removing alternate locations, water, and unwanted molecules using Home menu > Prepare. Preparing a purified system is essential for robust CG modeling. Prepare a protein system

  3. Launch Martinize2: Open the Martinize2 Extension from Home > Apps or via the Find Everything search functionality.

  4. Select Your Structure: In the SAMSON interface, select the desired molecular system for modeling. This ensures Martinize2 processes the exact input you want to work with. Select the structural model in the document

  5. Configure Martinize2 Settings: Choose your force field, position restraints, and other settings. Options like martini3001 for force fields and position restraint flexibility (backbone only, all, or none) allow customization suited to your specific task. Hover over options for additional tooltips for clarification. Martinize2 Options

  6. Specify Results Folder: Choose a destination for the outputs, which will include input PDB files, CG model files (PDB, GRO), and GROMACS topology files (.top and .itp).

  7. Create the CG Model: Click Create coarse-grained models, and Martinize2 will initiate the conversion. Progress is logged, and results are saved in a time-stamped folder for easy reference. If only one model is generated, it will automatically load into SAMSON for inspection.

Created CG model

Why Choose Martinize2 in SAMSON?

SAMSON’s interface simplifies and automates many steps required for CG modeling. From preparation to detailed configuration and final visualization, the Martinize2 Extension ensures accurate outputs while reducing manual effort.

Interested in Learning More?

If you’d like to explore the full potential of Martinize2 in SAMSON, including advanced features like generating CG models for multiple replicas or renumbering chains, check out the official documentation: Martinize2 Documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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