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51 bool bSet
; /* Has this combination been set */
52 real c
[3]; /* The non-bonded parameters */
54 /* The t_nbparam struct is used to temporary store the explicit
55 * non-bonded parameter combinations, which will be copied to t_params.
59 atom_id a
[MAXATOMLIST
]; /* The atom list (eg. bonds: particle */
60 /* i = a[0] (AI), j = a[1] (AJ)) */
61 real c
[MAXFORCEPARAM
]; /* Force parameters (eg. b0 = c[0]) */
62 char s
[MAXSLEN
]; /* A string (instead of parameters), *
63 * read from the .rtp file in pdb2gmx */
67 int nr
; /* The number of bonds in this record */
68 t_param
*param
; /* Array of parameters (dim: nr) */
72 int nr
; /* The number of exclusions */
73 atom_id
*e
; /* The excluded atoms */
78 int nrexcl
; /* Number of exclusions per atom */
79 bool excl_set
; /* Have exclusions been generated? */
80 bool bProcessed
; /* Has the mol been processed */
81 t_atoms atoms
; /* Atoms */
82 t_block cgs
; /* Charge groups */
83 t_block mols
; /* Molecules */
84 t_params plist
[F_NRE
]; /* Parameters in old style */
89 int nr
; /* The number of atomtypes */
90 t_atom
*atom
; /* Array of atoms */
91 char ***atomname
; /* Names of the atomtypes */
92 t_param
*nb
; /* Nonbonded force default params */
93 int *bondatomtype
; /* The bond_atomtype for each atomtype */
94 real
*radius
; /* Radius for GBSA stuff */
95 real
*vol
; /* Effective volume for GBSA */
96 real
*surftens
; /* Surface tension with water, for GBSA */
100 int nr
; /* Number of bond_atomtypes */
101 char ***atomname
; /* Names of the bond_atomtypes */
128 d_water_polarization
,
131 d_position_restraints
,
133 d_angle_restraints_z
,
134 d_distance_restraints
,
135 d_orientation_restraints
,
136 d_dihedral_restraints
,
142 static char *ds
[d_maxdir
+1] = {
152 /* All the directives above can not appear after moleculetype */
166 "water_polarization",
169 "position_restraints",
171 "angle_restraints_z",
172 "distance_restraints",
173 "orientation_restraints",
174 "dihedral_restraints",
178 extern void convert_harmonics(int nrmols
,t_molinfo mols
[],t_atomtype
*atype
);
180 #endif /* _grompp_h */