[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
>> some
>> 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
>> second
>> 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.

> Mark
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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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