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33 * GRoups of Organic Molecules in ACtion for Science
47 egcTC, egcENER, egcACC, egcFREEZE,
48 egcUser1, egcUser2, egcVCM, egcXTC,
54 char **name; /* Name of the molecule type */
55 t_atoms atoms; /* The atoms */
57 t_block cgs; /* The charge groups */
58 t_blocka excls; /* The exclusions */
62 int type; /* The molcule type index in mtop.moltype */
63 int nmol; /* The number of molecules in this block */
64 int natoms_mol; /* The number of atoms in one molecule */
65 int nposres_xA; /* The number of posres coords for top A */
66 rvec *posres_xA; /* The posres coords for top A */
67 int nposres_xB; /* The number of posres coords for top B */
68 rvec *posres_xB; /* The posres coords for top B */
72 t_grps grps[egcNR]; /* Groups of things */
73 int ngrpname; /* Number of groupnames */
74 char ***grpname; /* Names of the groups */
76 unsigned char *grpnr[egcNR]; /* Group numbers or NULL */
79 /* This macro gives the group number of group type egc for atom i.
80 * This macro is useful, since the grpnr pointers are NULL
81 * for group types that have all entries 0.
83 #define ggrpnr(groups,egc,i) ((groups)->grpnr[egc] ? (groups)->grpnr[egc][i] : 0)
85 /* The global, complete system topology struct, based on molecule types.
86 This structure should contain no data that is O(natoms) in memory. */
88 char **name; /* Name of the topology */
89 gmx_ffparams_t ffparams;
91 gmx_moltype_t *moltype;
93 gmx_molblock_t *molblock;
95 int maxres_renum; /* Parameter for residue numbering */
96 int maxresnr; /* The maximum residue number in moltype */
97 t_atomtypes atomtypes; /* Atomtype properties */
98 t_block mols; /* The molecules */
100 t_symtab symtab; /* The symbol table */
103 /* The mdrun node-local topology struct, completely written out */
105 t_idef idef; /* The interaction function definition */
106 t_atomtypes atomtypes; /* Atomtype properties */
107 t_block cgs; /* The charge groups */
108 t_blocka excls; /* The exclusions */
111 /* The old topology struct, completely written out, used in analysis tools */
113 char **name; /* Name of the topology */
114 t_idef idef; /* The interaction function definition */
115 t_atoms atoms; /* The atoms */
116 t_atomtypes atomtypes; /* Atomtype properties */
117 t_block cgs; /* The charge groups */
118 t_block mols; /* The molecules */
119 t_blocka excls; /* The exclusions */
120 t_symtab symtab; /* The symbol table */