3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
11 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
12 * Copyright (c) 2001-2004, The GROMACS development team,
13 * check out http://www.gromacs.org for more information.
15 * This program is free software; you can redistribute it and/or
16 * modify it under the terms of the GNU General Public License
17 * as published by the Free Software Foundation; either version 2
18 * of the License, or (at your option) any later version.
20 * If you want to redistribute modifications, please consider that
21 * scientific software is very special. Version control is crucial -
22 * bugs must be traceable. We will be happy to consider code for
23 * inclusion in the official distribution, but derived work must not
24 * be called official GROMACS. Details are found in the README & COPYING
25 * files - if they are missing, get the official version at www.gromacs.org.
27 * To help us fund GROMACS development, we humbly ask that you cite
28 * the papers on the package - you can find them in the top README file.
30 * For more info, check our website at http://www.gromacs.org
33 * Gromacs Runs On Most of All Computer Systems
40 #include "visibility.h"
51 gmx_bool bSet; /* Has this combination been set */
52 real c[4]; /* 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 int maxnr; /* The amount of elements in the array */
69 t_param *param; /* Array of parameters (dim: nr) */
71 /* CMAP tmp data, there are probably better places for this */
72 int grid_spacing; /* Cmap grid spacing */
73 int nc; /* Number of cmap angles */
75 real *cmap; /* Temporary storage of the raw cmap grid data */
76 int ncmap; /* Number of allocated elements in cmap grid*/
78 int *cmap_types; /* Store the five atomtypes followed by a number that identifies the type */
79 int nct; /* Number of allocated elements in cmap_types */
84 int nr; /* The number of exclusions */
85 atom_id *e; /* The excluded atoms */
90 int nrexcl; /* Number of exclusions per atom */
91 gmx_bool excl_set; /* Have exclusions been generated? */
92 gmx_bool bProcessed; /* Has the mol been processed */
93 t_atoms atoms; /* Atoms */
94 t_block cgs; /* Charge groups */
95 t_block mols; /* Molecules */
96 t_blocka excls; /* Exclusions */
97 t_params plist[F_NRE]; /* Parameters in old style */
105 GMX_LIBGMXPREPROCESS_EXPORT
106 gmx_bool is_int(double x);
107 /* Returns TRUE when x is integer */
118 d_implicit_genborn_params,
119 d_implicit_surface_params,
136 d_water_polarization,
137 d_thole_polarization,
140 d_position_restraints,
142 d_angle_restraints_z,
143 d_distance_restraints,
144 d_orientation_restraints,
145 d_dihedral_restraints,
152 static const char *ds[d_maxdir+1] = {
161 "implicit_genborn_params",
162 "implicit_surface_params",
164 /* All the directives above can not appear after moleculetype */
180 "water_polarization",
181 "thole_polarization",
184 "position_restraints",
186 "angle_restraints_z",
187 "distance_restraints",
188 "orientation_restraints",
189 "dihedral_restraints",
198 #endif /* _grompp_h */