[gmx-users] GROMACS OPLS-AA question
Barnett, James W
jbarnet4 at tulane.edu
Sat Sep 12 16:17:49 CEST 2015
On Thu, 2015-09-10 at 11:32 -0600, Eric Smoll wrote:
> 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
> 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
> 1, 2, and 3 bonds away with the following directive:
> [ moleculetype ]
> ; name nrexcl
> System 3
> 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
> "yes" as the third entry under the "[ defaults ]" directive.
> *Is this correct?*
Essentially this is correct. 1-2, 1-3, and 1-4 nonbonded interactions
are excluded when the number of exclusions is 3. With [ pairs ] and [
pairtypes ] 1-4 nonbonded interactions can be explicitly added back
(the point is that you 1-4 nonbonded interactions typically have
different parameters, so the normal non-bonded parameters for 1-4 are
excluded and then different parameters are added back with [pairs]).
OPLS doesn't do that, but instead generates the 1-4 nonbonded
interactions as specified in the [ defaults ] section.
> The manual states that "the use of [Ryckaert-Bellemans potential
> implies exclusion between the first and last atom of the dihedral."
> statement is referring to the use of nrexcl=3 in the "[ moleculetype
> directive as shown above, correct? The use of RB dihedral functions
> GROMACS does not imply that the scaled "pair" interactions are not
My understanding is it is saying 1-4 nonbonded interactions should be
excluded by setting nrexcl=3 when using RB dihedral functions. Clearly
OPLS uses the RB form in GROMACS and generates pairs, so pairs (either
generated or set with [ pairs ]), still apply.
That's my understanding - but you could test it out by setting generate
pairs to no in the [ defaults ] section and see if GROMACS complains
that [ pairs ] is missing even with the RB form of the potential. My
guess is that it will.
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow
Chemical and Biomolecular Engineering
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarnet4 at tulane.edu
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