[gmx-users] DPPC lipid model in Gromos 53a5
David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 3 14:24:03 CET 2008
Mark Abraham wrote:
>> Dear all,
>> In the definition of the DPPC lipid molecule in ffG53a5.rtp I found, that
>> dihedral angles are defined twice:
>> [ dihedrals ]
>> ; ai aj ak al gromos type
>> C33 N C32 C31 gd_29
>> N C32 C31 O32 gd_4
>> N C32 C31 O32 gd_36 <-
>> C32 C31 O32 P gd_29
>> C31 O32 P O31 gd_20
>> C31 O32 P O31 gd_27 <-
>> O32 P O31 C3 gd_20
>> O32 P O31 C3 gd_27 <-
>> Is this a mistake or on purpose ?
>> Does the second entry overwrite the first entry, i.e. the values of the
>> entry are used ?
> It depends on the functional form - you'll need to look up these gd_??
> macros in the forcefield .itp file. A second function with the same
> function type will over-write the first. I think it does so silently. A
> different function type on the same atoms is accepted silently.
I'm not sure this is correct: check your top file. If you have two
dihedrals in the top file both are evaluated and the effective
interaction is the sum of these. This is a way to fake a more
complicated dihedral term.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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