Hi, Section 4.2 of the manual has a discussion of dihedrals. The section contains, in part, the following text:
"With the periodic GROMOS potential a special 1-4 LJ-interaction must be included; with the Ryckaert-Bellemans potential _for alkanes_ the 1-4 interactions must be excluded from the non-bonded list. Note: Ryckaert-Bellemans potentials are also used in e.g. the OPLS force field in combination with 1-4 interactions. You should therefore not modify topologies generated by pdb2gmx in this case." I would like to ask in particular about the statement that "with the Ryckaert-Bellemans potential _for alkanes_ the 1-4 interactions must be excluded from the non-bonded list." Here are two questions about that statement: (1) Does that statement apply ONLY to the GROMOS force field, or does it apply to the OPLS-AA force field as well? (2) What is the meaning of "alkanes" in that statement? ----- (2a) Does it refer ONLY to saturated hydrocarbons, which contain only hydrogen and carbon and contain only single covalent bonds? (Examples of such molecules are butane, isobutane, pentane, isopentane, and hexane.) ----- (2b) Or, does it refer to ANY molecule which contains an alkyl group? (An example of such a molecule is the amino acid isoleucine. Isoleucine contains an alkyl group -- isoleucine's side chain is an isopentyl group. Does this mean that I need to EXCLUDE 1-4 interactions among hydrogens and carbons of the isopentyl group from the non-bonded list?) (3) In the OPLS-AA force field, nexcl is usually set to 3, which _initially_ excludes 1-4 interactions. However, in OPLS-AA, 1-4 interactions are explicitly specified in the [ pairs ] section; they are taken at half-strength by setting fudgeQQ = 0.5 and fudgeLJ = 0.5 in the topology. (See, for example, this helpful explanation: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/0 77005.html .) If the statement applies to OPLS-AA in addition to GROMOS, and if the statement applies to the alkyl atoms in, e.g. isoleucine, then do I need to EXCLUDE 1-4 interactions among isoleucine's hydrogens and carbons from the [ pairs ] section? Thank you for your time! Andrew DeYoung Carnegie Mellon University -- 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.