[gmx-users] Nonbonded interaction between two molecules

[Quyen Vu Van]

Dear Gromacs users,
I have a DNA molecule.
In PDB file two strands is separated by TER line, so pdb2gmx
separates my DNA as two molecules, each molecule has its topology file itp.
My question is whether the atoms in each strand have nonbonded interactions
with the other strand because as I understand that nonbonded interactions
are in [pairs] section in *.itp file
Thank you and best regards
Quyen