[gmx-users] GROMACS OPLS-AA question
ericsmoll at gmail.com
Thu Sep 10 19:32:18 CEST 2015
Hello GROMACS users,
I am interested in using the OPLS-AA as implemented in GROMACS.
The OPLS-AA forcefield omits all nonbonded (Coulomb and LJ) interactions 1
and 2 bonds away. Nonbonded interactions 3 bonds are away are scaled by
1/2. Nonbonded interactions are applied without modification for atoms 4 or
more bonds away or between atoms in different molecules.
In GROMACS, this is accomplished by excluding Coulomb and LJ interactions
1, 2, and 3 bonds away with the following directive:
[ moleculetype ]
; name nrexcl
The scaled intramolecular interaction at 3 bonds away is added in
separately as a "pair" interaction. This is either done manually with "[
pairtypes ]" and "[ pairs ]" directives or automatically by including
"yes" as the third entry under the "[ defaults ]" directive.
*Is this correct?*
The manual states that "the use of [Ryckaert-Bellemans potential functions]
implies exclusion between the first and last atom of the dihedral." *This
statement is referring to the use of nrexcl=3 in the "[ moleculetype ]"
directive as shown above, correct? The use of RB dihedral functions in
GROMACS does not imply that the scaled "pair" interactions are not applied,
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