annotate test-data/oplsaa.ff-tip4p.itp @ 16:3cf3b3b305ea draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"

;
; Note the strange order of atoms to make it faster in gromacs.
;
[ moleculetype ]
; molname	nrexcl
SOL		2

[ atoms ]
; id	at type	res nr 	residu name	at name	cg nr	charge
1       opls_113        1       SOL      OW     1       0.0
2       opls_114        1       SOL     HW1     1       0.52
3       opls_114        1       SOL     HW2     1       0.52
4       opls_115        1       SOL      MW     1      -1.04

#ifndef FLEXIBLE
[ settles ]
; OW    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

[ exclusions ]
1	2	3	4
2	1	3	4
3	1	2	4
4	1	2	3

; The position of the virtual site is computed as follows:
;
;		O
;  	      
;	    	D
;	  
;	H		H
;
; const = distance (OD) / [ cos (angle(DOH)) 	* distance (OH) ]
;	  0.015 nm	/ [ cos (52.26 deg)	* 0.09572 nm	]

; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)

[ virtual_sites3 ]
; Vsite from			funct	a		b
4	1	2	3	1	0.128012065	0.128012065