Center-of-Mass (COM) pulling simulations are a crucial technique for molecular modelers who want to investigate molecular interactions, structural stability, or force-dependent processes in biomolecules. However, setting up such simulations can often feel tedious and error-prone. This is where SAMSON’s GROMACS Wizard simplifies the process, enabling researchers to intuitively set up and execute COM pulling simulations with ease. In this blog post, we’ll walk you through how to set up a COM pulling simulation using chain interactions from SAMSON’s GROMACS Wizard, highlighting tips and options that can save you significant time.
Why COM Pulling?
COM pulling allows you to study the mechanical response of biomolecular systems by applying a controlled force to one component (e.g., a protein chain) relative to another part of the system. For instance, in the example system used here (PDB: 2BEG), chain A is pulled away from chain B in the z-direction to simulate the molecular dynamics of chain separation.
Setting Up the System
The GROMACS Wizard is designed to simplify the steps of a COM pulling simulation. First, you load your system (e.g., 2BEG) into SAMSON. You can do this via Home > Fetch, entering the PDB ID, and clicking “Load.” You’ll then see the structural model and trajectory in the Document view and Viewport, which can be refined and reoriented to visualize the required molecular chains effectively.
Next, SAMSON allows you to navigate through multiple conformations of the system’s trajectory to select the ideal starting conformation. This inspection can be easily performed using the Inspector tool.
Preparing the System and Defining the Pulling Box
Once the initial inspection is done, you move to preparation. Here’s an essential consideration: leave enough space in the pulling direction to ensure smooth simulations. In this example, chain A is pulled away from chain B in the z-direction for a distance of 5 nm. The box size in the z-direction is configured to at least 12 nm to ensure compliance with the minimum image convention. SAMSON makes this process incredibly manageable with its intuitive controls for box size and configuration.
Neutralizing the System
A key step in accurate molecular simulations is ensuring that your system is charge-neutral. In SAMSON, this is achieved by adding neutralizing ions (e.g., Na+ and Cl–) along with a specific salt concentration. For this example, a 100 mM NaCl concentration is added to the system alongside neutralizing counterions, enabling realistic electrostatic interactions during the simulation.
Executing the Pulling Simulation
The cornerstone of this tutorial is setting up the COM pulling parameters in the production MD step. SAMSON’s GROMACS Wizard offers a clear and structured interface for specifying pulling parameters:
- Type: umbrella
- Pull direction: z-axis
- Pull rate: 0.01 nm/ps
- Force constant: 1000 kJ mol-1 nm-2
By leveraging these settings, chain A is pulled from chain B while restrained forces allow observations of molecular interactions and force evolution over time.
Visualizing the Results
Once the calculation is complete, you can visualize the pulling trajectory in SAMSON to gain insights into the molecular behavior under mechanical force. SAMSON also generates force-displacement plots that illustrate the evolution of pulling forces during the simulation. These are invaluable for analyzing the system’s mechanical responses and characterizing specific force-dependent phenomena.
Conclusion
Combining SAMSON’s GROMACS Wizard with its intuitive tools and user-friendly interface significantly reduces the effort needed for complex setups like COM pulling. Whether you’re a beginner or an advanced researcher, SAMSON empowers you to explore molecular dynamics simulations with confidence. To dive deeper into this tutorial and explore additional resources, visit the original SAMSON documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.