; Gromacs topology for 1-octanol
; (to be used with ffgmxbon.itp and ffgmxnbon.itp --- but really the
; Tieleman lipid parameters)
;
; Source: Magdalena Elzbieta Siwko, "Disturb or stabilise? Effects of different
;         molecules on biological membranes", Rijksuniversiteit Groningen 2008
;
; copied & pasted from 
; http://dissertations.ub.rug.nl/FILES/faculties/science/2008/m.e.siwko/06_appendix.pdf
; and comment characters added where necessary (OB 2009-08-12)
;
; Validation (as shown in the thesis):
;      MD density (neat octanol at 298K): 829.1 +/- 0.1 g/l
;      experiment [1]: 827 g/l 
;
;      [1] CRC handbook of chemistry and physics, 67th Edition, R. C. Weast
;          (Ed.), CRC Press, Boca Raton, Florida, 1987.

[ moleculetype ] 
; Name nrexcl 
Octanol 3 

[atoms] 
;nr type resnr residu atom cgnr charge
1 LP3 1 OCT C1 1 0.0 
2 LP2 1 OCT C2 2 0.0 
3 LP2 1 OCT C3 3 0.0 
4 LP2 1 OCT C4 4 0.0 
5 LP2 1 OCT C5 5 0.0 
6 LP2 1 OCT C6 6 0.0 
7 LP2 1 OCT C7 7 0.0 
8 LP2 1 OCT C8 8 0.156 
9 OA 1 OCT O9 8 -0.563 
10 HO 1 OCT H10 8 0.407 

[bonds] 
; ai aj func b0 cb 
1 2 1 0.15300E+00 0.33470E+06 
2 3 1 0.15300E+00 0.33470E+06 
3 4 1 0.15300E+00 0.33470E+06 
4 5 1 0.15300E+00 0.33470E+06 
5 6 1 0.15300E+00 0.33470E+06 
6 7 1 0.15300E+00 0.33470E+06 
7 8 1 0.15300E+00 0.33470E+06 
8 9 1 0.12300E+00 0.50210E+06 
9 10 1 

[angles] 
; ai aj ak func th0 cth 
1 2 3 1 0.11100E+03 0.46020E+03 
2 3 4 1 0.11100E+03 0.46020E+03 
3 4 5 1 0.11100E+03 0.46020E+03 
4 5 6 1 0.11100E+03 0.46020E+03 
5 6 7 1 0.11100E+03 0.46020E+03 
6 7 8 1 0.11100E+03 0.46020E+03 
7 8 9 1 0.12100E+03 0.50210E+03 
8 9 10 1 0.10950E+03 0.39748E+03 

[dihedrals] 
; ai aj ak al func 
1 2 3 4 3 
2 3 4 5 3 
3 4 5 6 3 
4 5 6 7 3
5 6 7 8 3 

[dihedrals] 
;ai aj ak al func phi0 cphi mult 
6 7 8 9 1 0.000 1.255 3 
7 8 9 10 1 0.000 1.255 3 
1831