PDB2GMX, structure too large

[alevilla]

Hi,
Maybe the solution discussed in the post below, works also in your case.

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 …

\Alessandra