When preparing a molecular system for simulation, understanding the role of position restraints during the NPT (constant pressure and temperature) equilibration phase can save you time—and help you avoid unexpected behavior in your trajectories.
This post walks you through how to handle position restraints with SAMSON’s GROMACS Wizard during the NPT equilibration step. It’s a small detail that can make a big difference, especially when dealing with large multi-chain complexes where specific regions must remain fixed.
Why use position restraints?
Position restraints allow you to apply a force that keeps specific atoms (usually heavy atoms or whole molecules) relatively static during equilibration. This is especially helpful when:
- You’ve just solvated your system and want to avoid movement of the core structure while the solvent equilibrates around it.
- You are preparing a pulling simulation and need to immobilize one chain while applying forces to another.
- You want to prevent distortion of binding sites or other functionally relevant regions.
By default, the GROMACS Wizard automatically identifies chains and water molecules that can be restrained. But what if you want to review or tweak those settings? Let’s take a closer look.
How to apply position restraints with GROMACS Wizard
Once you arrive at the NPT Equilibration stage (Step 5 in your simulation pipeline), switch to the Equilibrate (NPT) tab in the GROMACS Wizard.
Click the Auto-Fill button to initialize from the previous step. Then open advanced settings by clicking the All… button in the Parameters section. This reveals detailed options, including those related to position restraints.
In the Preprocessing section, you will see POSRES options for each chain and for water. Enabling position restraints for specific chains means those chains will remain in place throughout the equilibration.
In the example below, both chain A (the pulled chain) and chain B (the restrained chain) are available. For NPT equilibration, it makes sense to keep chain B restrained to maintain stability while the surrounding environment adjusts.
What about temperature settings?
In the Temperature Coupling section, set the system temperature (usually 310 K for simulations mimicking physiological conditions).
Make sure the value matches in the Velocity Generation section as well:
Running the equilibration
Once you’re satisfied with the parameters, click the Equilibrate locally button. The simulation will run in the background, thanks to the integrated job manager.
When it’s complete, you’ll have access to plots showing how density, temperature, and pressure stabilized during the run.
Conclusion
Using position restraints correctly during NPT equilibration can improve the stability of your system and allow the solvent to relax without disturbing key components of your biomolecule. SAMSON’s GROMACS Wizard makes it easy to apply and tailor restraints, especially as part of larger workflows like COM pulling or umbrella sampling.
To learn more, including how to proceed with the next stages like production MD simulation, see the full tutorial at this page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.