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38 #ifndef GMX_GMXPREPROCESS_GROMPP_IMPL_H
39 #define GMX_GMXPREPROCESS_GROMPP_IMPL_H
50 gmx_bool bSet; /* Has this combination been set */
51 real c[4]; /* The non-bonded parameters */
53 /* The t_nbparam struct is used to temporary store the explicit
54 * non-bonded parameter combinations, which will be copied to t_params.
58 atom_id a[MAXATOMLIST]; /* The atom list (eg. bonds: particle */
59 /* i = a[0] (AI), j = a[1] (AJ)) */
60 real c[MAXFORCEPARAM]; /* Force parameters (eg. b0 = c[0]) */
61 char s[MAXSLEN]; /* A string (instead of parameters), *
62 * read from the .rtp file in pdb2gmx */
66 int nr; /* The number of bonds in this record */
67 int maxnr; /* The amount of elements in the array */
68 t_param *param; /* Array of parameters (dim: nr) */
70 /* CMAP tmp data, there are probably better places for this */
71 int grid_spacing; /* Cmap grid spacing */
72 int nc; /* Number of cmap angles */
74 real *cmap; /* Temporary storage of the raw cmap grid data */
75 int ncmap; /* Number of allocated elements in cmap grid*/
77 int *cmap_types; /* Store the five atomtypes followed by a number that identifies the type */
78 int nct; /* Number of allocated elements in cmap_types */
83 int nr; /* The number of exclusions */
84 atom_id *e; /* The excluded atoms */
89 int nrexcl; /* Number of exclusions per atom */
90 gmx_bool excl_set; /* Have exclusions been generated? */
91 gmx_bool bProcessed; /* Has the mol been processed */
92 t_atoms atoms; /* Atoms */
93 t_block cgs; /* Charge groups */
94 t_block mols; /* Molecules */
95 t_blocka excls; /* Exclusions */
96 t_params plist[F_NRE]; /* Parameters in old style */
104 gmx_bool is_int(double x);
105 /* Returns TRUE when x is integer */
107 /* Must correspond to strings in topdirs.c */
117 d_implicit_genborn_params,
118 d_implicit_surface_params,
135 d_water_polarization,
136 d_thole_polarization,
139 d_position_restraints,
141 d_angle_restraints_z,
142 d_distance_restraints,
143 d_orientation_restraints,
144 d_dihedral_restraints,