GROMACS version: 2025.2
GROMACS modification: No
Hi everyone,
I am struggling with PBC wrapping artifacts in a system involving a protein-ligand (GTP) complex interacting with a Laponite clay surface**(infinite sheet)**. My goal is to achieve trajectory wrapping, in a way that I will have protein and gtp centered in xy place while having fixed clay slab on z direction. When I am trying to do nojump or cluster this infinite slab is resulting in a “starburst” artifact, and if I do minimal wrapping the protein and ligand dissociating across periodic boundaries.
The Problem: When I attempt to make the complex whole and centered, the trajectory exhibits extreme visual artifacts where atoms are pulled across the box. I am currently using a multi-step trjconv approach:
-
-pbc mol -
-pbc cluster -
-ur compact
Even after clustering the complex (Protein+GTP+Mg) and compacting the unit cell, the protein and the ligand (GTP) appear to separate or “glide” independently across periodic boundaries, preventing accurate interaction analysis.
My main Question is Surface Clustering strategy: Since the LAP surface is effectively a infinite molecule, how can I center the Protein-Ligand complex in XY while keeping the slab intact? Or is there an accepted way how people would wrap systems including infinite molecules?
I have tried trjconv -pbc mol followed by cluster and compact and Various manual index group selections to keep LAP intact, but I could never keep protein ligand slab and water all happy.
I would appreciate any guidance on the standard workflow for these types of surface-adsorption simulations.
Best,
Gvantsa