Gromacs  2016.4
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Functions
#include <stdio.h>
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/basedefinitions.h"
+ Include dependency graph for bonded.h:

Description

This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions.

Author
Mark Abraham mark..nosp@m.j.ab.nosp@m.raham.nosp@m.@gma.nosp@m.il.co.nosp@m.m

Functions

real bond_angle (const rvec xi, const rvec xj, const rvec xk, const struct t_pbc *pbc, rvec r_ij, rvec r_kj, real *costh, int *t1, int *t2)
 Calculate bond-angle. No PBC is taken into account (use mol-shift)
 
real dih_angle (const rvec xi, const rvec xj, const rvec xk, const rvec xl, const struct t_pbc *pbc, rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, real *sign, int *t1, int *t2, int *t3)
 Calculate dihedral-angle. No PBC is taken into account (use mol-shift)
 
void do_dih_fup (int i, int j, int k, int l, real ddphi, rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, rvec4 f[], rvec fshift[], const struct t_pbc *pbc, const struct t_graph *g, const rvec *x, int t1, int t2, int t3)
 Do an update of the forces for dihedral potentials.
 
void make_dp_periodic (real *dp)
 Make a dihedral fall in the range (-pi,pi)
 
real cmap_dihs (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const gmx_cmap_t *cmap_grid, const rvec x[], rvec4 f[], rvec fshift[], const struct t_pbc *pbc, const struct t_graph *g, real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index)
 Compute CMAP dihedral energies and forces.