[gmx-users] Nonbonded interaction between two molecules
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.
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
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