GROMACS Tips and Tricks: How to remove GROMACS periodic boundary conditions?

GROMACS is a popular molecular dynamics simulation software that uses periodic boundary conditions (PBC) to minimize edge effects and errors in finite systems.

However, sometimes you may want to simulate a non-periodic system, such as a liquid or a solution, without the artificial periodicity imposed by PBC. In this case, you need to know how to remove GROMACS PBC and convert the output trajectory to a different unit-cell representation.

There are several methods and tools that can help you with this task. Here are some of them:

• One method is to use the gmx trjconv command with the -pbc mol option to convert the whole molecule into a brick-shaped volume, and then use the -ur compact option to center the molecule on interfacial residues belonging to one monomer. This will put the interface of the dimer at (or at least, extremely close to) the center of the box, with both monomers in the unit cell¹.Another method is to use the gmx trjconv command with the -pbc mol -ur compact -center options to remove PBC and center the molecule on interfacial residues belonging to one monomer². This will also generate some frames with two chains on different sides of the box, instead of a “whole”. You can then use another tool, such as gmx trjconv, gmx trjconv -pbc mol -ur compact, or gmx trjconv -pbc mol -ur compact -center, to convert these frames into a different unit-cell representation.
• A third method is to use a custom index group that selects only interfacial residues belonging to one monomer, and then use gmx trjconv with this index group as an input file. This will also put both monomers in the unit cell and remove PBC¹.
• A fourth method is to modify your input file manually and set periodic=False for each chain that you want to simulate without PBC. This will also require you to specify your own unit-cell parameters using box_vectors. You can then use gmx trjconv with your modified input file as an output file³.

These are some of the possible ways to remove GROMACS PBC and convert your output trajectory into a different unit-cell representation.

Exploring Alternative Approaches: The MDVWhole Program
The MDVWhole program is an alternative method to remove periodic boundary conditions in GROMACS simulations. It provides a different approach compared to the commonly used "trjconv" command.

One of the key strengths of MDVWhole is its ability to handle more complex systems that may pose challenges for "trjconv". For example, if your simulation involves non-standard box shapes or highly anisotropic systems, MDVWhole can handle them effectively. It allows for more flexibility in defining and manipulating the unit cell representation.

Additionally, MDVWhole offers advanced features for dealing with special cases. For instance, it can accurately handle simulations involving flexible molecules or non-equidistant sampling of molecular conformations.

In summary, while "trjconv" remains the go-to method for most users due to its simplicity and widespread availability, the MDVWhole program offers an alternative approach with added capabilities for handling complex systems and special cases. Depending on your specific simulation requirements, it may be worth exploring MDVWhole as an alternative to achieve more accurate and reliable results.

You can find more details and examples in these sources:

• 1- Periodic boundary conditions — GROMACS 2019-rc1 documentation, 
• 2- How to remove GROMACS periodic boundary conditions? - FAQS.TIPS,
• 3- Add feature somewhere to remove periodic boundary conditions for …, 
• 4- Algorithm Gromacs used for removing periodic boundary condition.

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Tags: GROMACS, Molecular dynamics