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33 * GRoups of Organic Molecules in ACtion for Science
42 typedef real rvec5[5];
44 /* Distance restraining stuff */
46 int dr_weighting; /* Weighting of pairs in one restraint */
47 gmx_bool dr_bMixed; /* Use sqrt of the instantaneous times *
48 * the time averaged violation */
49 real dr_fc; /* Force constant for disres, *
50 * which is multiplied by a (possibly) *
51 * different factor for each restraint */
52 real dr_tau; /* Time constant for disres */
53 real ETerm; /* multiplication factor for time averaging */
54 real ETerm1; /* 1 - ETerm1 */
55 real exp_min_t_tau; /* Factor for slowly switching on the force */
56 int nres; /* The number of distance restraints */
57 int npair; /* The number of distance restraint pairs */
58 real sumviol; /* The sum of violations */
59 real *rt; /* The calculated instantaneous distance (npr) */
60 real *rm3tav; /* The calculated time averaged distance (npr) */
61 real *Rtl_6; /* The calculated instantaneous r^-6 (nr) */
62 real *Rt_6; /* The calculated inst. ens. averaged r^-6 (nr) */
63 real *Rtav_6; /* The calculated time and ens. averaged r^-6 (nr) */
64 int nsystems; /* The number of systems for ensemble averaging */
65 MPI_Comm mpi_comm_ensemble; /* For ensemble averaging */
69 /* Orientation restraining stuff */
71 real fc; /* Force constant for the restraints */
72 real edt; /* Multiplication factor for time averaging */
73 real edt_1; /* 1 - edt */
74 real exp_min_t_tau; /* Factor for slowly switching on the force */
75 int nr; /* The number of orientation restraints */
76 int nex; /* The number of experiments */
77 int nref; /* The number of atoms for the fit */
78 real *mref; /* The masses of the reference atoms */
79 rvec *xref; /* The reference coordinates for the fit (nref) */
80 rvec *xtmp; /* Temporary array for fitting (nref) */
81 matrix R; /* Rotation matrix to rotate to the reference coor. */
82 tensor *S; /* Array of order tensors for each experiment (nexp) */
83 rvec5 *Dinsl; /* The order matrix D for all restraints (nr x 5) */
84 rvec5 *Dins; /* The ensemble averaged D (nr x 5) */
85 rvec5 *Dtav; /* The time and ensemble averaged D (nr x 5) */
86 real *oinsl; /* The calculated instantaneous orientations */
87 real *oins; /* The calculated emsemble averaged orientations */
88 real *otav; /* The calculated time and ensemble averaged orient. */
89 real rmsdev; /* The weighted (using kfac) RMS deviation */
90 rvec5 *tmp; /* An array of temporary 5-vectors (nex); */
91 real ***TMP; /* An array of temporary 5x5 matrices (nex); */
92 real *eig; /* Eigenvalues/vectors, for output only (nex x 12) */
94 /* variables for diagonalization with diagonalize_orires_tensors()*/
101 * Data struct used in the force calculation routines
102 * for storing the tables for bonded interactions and
103 * for storing information which is needed in following steps
104 * (for instance for time averaging in distance retraints)
105 * or for storing output, since force routines only return the potential.
108 bondedtable_t *bondtab;
109 bondedtable_t *angletab;
110 bondedtable_t *dihtab;