/usr/share/gromacs/top/oplsaa.ff/tip5p.itp is in gromacs-data 2018.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 | ; original reference: [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112 , 2000]
;
; Note that there are various issues with tip5p and the different forcefields.
; Discussion is here: http://redmine.gromacs.org/issues/1348
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 opls_118 1 SOL OW 1 0
2 opls_119 1 SOL HW1 1 0.241
3 opls_119 1 SOL HW2 1 0.241
4 opls_120 1 SOL LP1 1 -0.241
5 opls_120 1 SOL LP2 1 -0.241
#ifndef FLEXIBLE
[ settles ]
; i funct doh dhh
1 1 0.09572 0.15139
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 502416.0 0.09572 502416.0
1 3 1 0.09572 502416.0 0.09572 502416.0
[ angles ]
; i j k funct angle force.c.
2 1 3 1 104.52 628.02 104.52 628.02
#endif
[ virtual_sites3 ]
; The position of the virtual site is computed as follows:
;
; The distance from OW to L is 0.07 nm, the geometry is tetrahedral
; (109.47 deg)
; Therefore, a = b = 0.07 * cos (109.47/2) / | xOH1 + xOH2 |
; c = 0.07 * sin (109.47/2) / | xOH1 X xOH2 |
;
; Using | xOH1 X xOH2 | = | xOH1 | | xOH2 | sin (H1-O-H2)
; | xOH1 + xOH2 | = 2 | xOH1 | cos (H1-O-H2)
; Vsite pos x4 = x1 + a*x21 + b*x31 + c*(x21 X x31)
; Vsite from funct a b c
4 1 2 3 4 -0.344908 -0.344908 -6.4437903493
5 1 2 3 4 -0.344908 -0.344908 6.4437903493
[ exclusions ]
1 2 3 4 5
2 1 3 4 5
3 1 2 4 5
4 1 2 3 5
5 1 2 3 4
|