[gmx-users] Questions about 1-4 interactions in alkanes

Andrew DeYoung 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!

Andrew DeYoung
Carnegie Mellon University

More information about the gromacs.org_gmx-users mailing list