[gmx-users] Type 9 dihedral in Gromacs topology
Peter C. Lai
pcl at uab.edu
Sat Oct 27 21:37:26 CEST 2012
On 2012-10-27 01:20:15PM -0400, Andrew DeYoung wrote:
> (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?
It means what it says. Look at the charmm's ffbonded.itp file closely again,
in the dihedral section. You will see that for each combination of dihedral
angles, you can have multiple potentials defined with different
multiplicities. In a non-type 9 dihedral potential gromacs would complain
about a second dihedral definition for the same dihedral and override the
CE2 CE1 CT2 CT3 9 180.00 2.092 1
CE2 CE1 CT2 CT3 9 180.00 5.4392 3
> (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?
Yes, although the CHARMM people call it KChi.
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
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