[gmx-users] Nonbonded interaction between two molecules

[Quyen Vu Van]

Dear Justin
that's clear,
Thank you

On Tue, Nov 27, 2018 at 5:16 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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