4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
12 * Copyright (c) 1991-1999
13 * BIOSON Research Institute, Dept. of Biophysical Chemistry
14 * University of Groningen, The Netherlands
17 * GROMACS: A message-passing parallel molecular dynamics implementation
18 * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
19 * Comp. Phys. Comm. 91, 43-56 (1995)
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34 typedef enum {eStart, eAfm, eConstraint, eUmbrella, eTest} t_runtype;
35 typedef enum {eCom, eComT0, eDyn, eDynT0} t_reftype;
38 int n; /* number of groups */
39 atom_id **idx; /* indices of pull atoms in full coordinate array */
40 real **weights; /* position depended weight (switch function) */
41 int *ngx; /* pull group sizes */
42 char **grps; /* pull group names */
43 real *tmass; /* total mass of the groups */
44 rvec **x0; /* pull group coordinates at t=0 */
45 rvec **xp; /* pull group coordinates at previous step */
46 rvec *x_ref; /* reference positions */
47 rvec *x_unc; /* center of mass before constraining */
48 rvec *x_con; /* center of mass, obeying constraints */
49 rvec *xprev; /* position of coms in last written structure */
50 rvec *f; /* forces due to the pulling/constraining */
51 rvec *spring; /* coordinates of the springs (eAfm) */
52 rvec *dir; /* direction of constraint */
53 real *d_ref; /* reference distance */
54 rvec *xtarget; /* target coordinates for structure generation */
55 rvec **comhist; /* com over the last nhist steps (for running aver) */
59 t_pullgrps dyna; /* dynamic groups for use with local constraints */
60 t_pullgrps pull; /* groups to pull/restrain/etc/ */
61 t_pullgrps ref; /* reference group, reaction force grps */
62 t_runtype runtype; /* start, afm, constraint, umbrella, test */
63 t_reftype reftype; /* com, com_t0, dynamic, dynamic_t0 */
64 rvec dims; /* used to select components for constraint */
65 rvec coor; /* reaction coordinate */
66 real r; /* radius of cylinder for dynamic COM */
67 real rc; /* radius of cylinder including switch length */
68 int bRot[3]; /* rotation around x, y, z? */
69 real rot_rate; /* rate of rotation, for startstructure run */
70 real xlt_rate; /* rate of translation, for startstructure run */
71 int rot_incr; /* write out structure every rot_incr degrees */
72 real xlt_incr; /* write out structure every xlt_incr nm */
73 real tolerance; /* tolerance for reaching desired coordinates (nm) */
74 real constr_tol;/* absolute tolerance for constraints in (nm) */
75 bool bPull; /* true if we're doing any pulling */
76 bool bCyl; /* true if we're using dynamic ref. groups */
77 bool bReverse; /* reverse reference direction */
78 FILE *out; /* output file for pull data */
79 real k; /* force constant for atoms */
80 real rate; /* pull rate, in nm/timestep */
81 real um_width; /* width umbrella potential */
82 int update; /* update frequency for dynamic grps */
83 int reflag; /* running average over reflag steps for com */
84 bool bVerbose; /* be loud and noise */