[gmx-users] Type 9 dihedral in Gromacs topology

Andrew DeYoung adeyoung at andrew.cmu.edu
Sat Oct 27 19:20:15 CEST 2012


This question is a sequel of sorts to my earlier question about dihedral
parameters in Gromacs

I typically use the OPLS-AA force field.  In OPLS-AA, dihedrals are usually
specified with the Ryckaert-Bellemans function.  In Table 5.5 on page 125 of
Section 5.7 of the manual, such a Ryckaert-Bellemans function specification
is called a type 3 dihedral.  This is why there is a 3 in the function type
column in the dihedral section of the OPLS-AA ffbonded.itp file.

One can also use type 1 dihedrals, which, as shown in the manual, have the
simple potential energy form V_d(phi_ijkl) = k_phi (1 + cos(n*phi - phi_s)).

However, in the CHARMM force field ffbonded.itp file included in Gromacs, it
seems that all of the [ dihedraltypes ] are specified using dihedral
function type 9.  Here is an example from the CHARMM ffbonded.itp:

; i     j       k       l       func    phi0    cp      mult
C       CT1     NH1     C       9       180.00  0.8368  1

If you have time, I have two questions about type 9 dihedral functions:

(1) What is a type 9 dihedral?  On page 74 of Section 4.2.12 of the manual,
it says, "For certain force fields, type 9 is useful.  Type 9 allows
multiple potential functions to be applied automatically to a single
dihedral in the [ dihedral ] section when multiple parameters are defined
for the same atomtypes in the [ dihedraltypes ] section."  What does this
mean?  What does it mean to apply multiple potential functions to a single
dihedral?  Is this a fundamentally different way of specifying a dihedral?

(2) In that above example from the CHARMM ffbonded.itp, what is the "cp"
column?  Table 5.5 of on page 125 of Section 5.7 of the manual seems to say
that in type 9, phi_s, k_phi, and the multiplicity are specified.  Does this
mean that "cp" corresponds to the force constant k_phi?

Thank you for your time!

Andrew DeYoung
Carnegie Mellon University

More information about the gromacs.org_gmx-users mailing list