[gmx-users] DPPC lipid model in Gromos 53a5
a.kukol at herts.ac.uk
Mon Mar 3 10:06:44 CET 2008
The gd_?? macros are
#define gd_4 180.000 5.86 1
; N-CHn-CHn-OA (lipid) 1.4
#define gd_36 0.000 8.62 3
; N-CHn-CHn-OA (lipid) 2.1
#define gd_20 0.000 5.09 2
; O-P-O- (dna, lipids) 1.2
#define gd_27 0.000 3.19 3
; O-P-O- (dna, lipids) 0.8
The two repeating dihedral definitions are certainly in the .top file, because I
have copied the DPPC definition from ffG53a5.rtp into an .itp file as a
starting point for developing a 'good' DPPC model consistent with the Gromos
53a5 force field.
Many thanks for your comments
David van der Spoel wrote:
> Mark Abraham wrote:
>>> Dear all,
>>> In the definition of the DPPC lipid molecule in ffG53a5.rtp I found,
>>> 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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