Periodic molecules - infinite graphene layer

[alevilla]

Hi,

“periodic-molecule = yes” in .mdp file does not generate bond potential automatically between the image, you have to manually including them in the topology file

This post on DNA may also help

Infinite DNA (across boundary conditions)

GROMACS version: 2021 GROMACS modification: No Hi fellow GROMACSers, I am trying to simulate an infinite DNA using periodic boundary conditions. I have used a process that I believe was suggested by @jalemkul in a previous version of the gromacs forum, but it is very likely that I misunderstood it. I first created generated a 12bp DNA pdb (Using this website: Sequence to Structure . If there are better ways of doing this, please offer suggestions.) I then ran it through pdb2gmx to create a …

Best regards
Alessandra