Simulating an Infinite polymer across boundaries

User discussions
1

GROMACS version: 2025.1
GROMACS modification: No

Hi all,

I am trying to simulate an infinite sugar polymer across periodic boundaries. I generated the initial structure in CHARMM using the standard 14BB patch. To mimic an infinite polymer, I connected the first and last sugar residues with the same 14BB patch. The long bond spanning the terminal residues is present in the CHARMM PSF file.

After converting the CHARMM PSF/CRD files to GROMACS format and setting up periodic boundary conditions, I obtain a periodic system. However, I do not see the bonds between periodic neighbors when visualizing the system.

I found a few previous forum posts where users manually added the periodic connections to the topology. In my case, however, all the required bonded interactions (bonds, angles, etc.) are already present in the topology and are included in the .tpr file. Despite this, I am unable to visualize the polymer as an “infinite” chain across the box boundaries.

To test the setup, I performed a quick energy minimization followed by a very short equilibration using periodic-molecules = yes. The resulting .tpr file still contains the periodic bonded interactions, but they are not displayed across the box edges.

Is there something wrong with my setup, or is this simply a visualization issue? I have attached the .gro, and .tpr files for reference.

Thanks in advance for any suggestions.

image
image671×729 7.83 KB

system_tpr.dat (80.8 KB)

system_gro.dat (126.0 KB)

2

This sounds like a visualization issue. You don’t mention which program you use to visualize and what input you use. Many programs display bonds based on distance, so those will not show bonds over periodic boundaries.