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 > 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 > 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 > including > "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 > 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, > correct?* 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 Tulane University 341-B Lindy Boggs Center for Energy and Biotechnology 6823 St. Charles Ave New Orleans, Louisiana 70118-5674 jbarn...@tulane.edu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.