[gmx-users] Nonbonded interaction between two molecules

[Justin Lemkul]

On 11/27/18 11:14 AM, Quyen Vu Van wrote:
> 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

Pairs define only 1-4 intramolecular nonbonded interactions. Everything 
else experiences nonbonded interactions based on which atoms fall within 
the nonbonded radius set in the .mdp file.

-Justin

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Justin A. Lemkul, Ph.D.
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