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 first. Example: 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 [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
