[gmx-users] Questions about 1-4 interactions in alkanes
adeyoung at andrew.cmu.edu
Sat Aug 23 23:17:45 CEST 2014
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
(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:
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!
Carnegie Mellon University
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