[gmx-users] Nonbonded interaction between two molecules

Justin Lemkul jalemkul at vt.edu
Tue Nov 27 17:16:22 CET 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list