src/gromacs/listed_forces/restcbt.h

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  35
  36 /*! \internal \file
  37  *
  38  *
  39  * \brief
  40  * This file contains function declarations necessary
  41    for computations of forces due to restricted angle, restricted dihedral and
  42    combined bending-torsion potentials.
  43  *
  44  * \author Nicolae Goga
  45  *
  46  * \ingroup module_listed_forces
  47  */
  48
  49 #ifndef GMX_LISTED_FORCES_RESTCBT_H
  50 #define GMX_LISTED_FORCES_RESTCBT_H
  51
  52 #include "gromacs/math/vec.h"
  53 #include "gromacs/topology/idef.h"
  54 #include "gromacs/utility/real.h"
  55
  56 /*! \brief This function computes factors needed for restricted angle potentials.
  57  *
  58  * The restricted angle potential is used in coarse-grained simulations to avoid singularities
  59  * when three particles align and the dihedral angle and dihedral potential cannot be calculated.
  60  * This potential is calculated using the formula:
  61  * \f[V_{\rm ReB}(\theta_i) = \frac{1}{2} k_{\theta} \frac{(\cos\theta_i - \cos\theta_0)^2}{\sin^2\theta_i}\f]
  62  * (see section "Restricted Bending Potential" from the manual).
  63  * The derivative of the restricted angle potential is calculated as:
  64  * \f[\frac{\partial V_{\rm ReB}(\theta_i)} {\partial \vec r_{k}} = \frac{dV_{\rm ReB}(\theta_i)}{dcos\theta_i} \frac{\partial cos\theta_i}{\partial \vec r_{k}}\f]
  65  * where all the derivatives of the bending angle with respect to Cartesian coordinates are calculated as in Allen & Tildesley (pp. 330-332)
  66  *
  67  *  \param[in]  type           type of force parameters
  68  *  \param[in]  forceparams    array of parameters for force computations
  69  *  \param[in]  delta_ante     distance between the first two particles
  70  *  \param[in]  delta_post     distance between the last two particles
  71  *  \param[out] prefactor      common term that comes in front of each force
  72  *  \param[out] ratio_ante     ratio of scalar products of delta_ante with delta_post
  73                               and delta_ante with delta_ante
  74  *  \param[out] ratio_post    ratio of scalar products of delta_ante with delta_post
  75                               and delta_post with delta_ante
  76  *  \param[out] v              contribution to energy   (see formula above)
  77  */
  78
  79
  80 void compute_factors_restangles(int type, const t_iparams forceparams[],
  81                                 rvec delta_ante,  rvec delta_post,
  82                                 double *prefactor, double *ratio_ante, double *ratio_post, real *v);
  83
  84
  85 /*! \brief Compute factors for restricted dihedral potentials.
  86  *
  87  * The restricted dihedral potential is the equivalent of the restricted bending potential
  88  * for the dihedral angle. It imposes the dihedral angle to have only one equilibrium value.
  89  * This potential is calculated using the formula:
  90  * \f[V_{\rm ReT}(\phi_i) = \frac{1}{2} k_{\phi} \frac{(\cos\phi_i - \cos\phi_0)^2}{\sin^2\phi_i}\f]
  91  * (see section "Proper dihedrals: Restricted torsion potential" from the manual).
  92  * The derivative of the restricted dihedral potential is calculated as:
  93  * \f[\frac{\partial V_{\rm ReT}(\phi_i)} {\partial \vec r_{k}} = \frac{dV_{\rm ReT}(\phi_i)}{dcos\phi_i} \frac{\partial cos\phi_i}{\partial \vec r_{k}}\f]
  94  * where all the derivatives of the dihedral angle with respect to Cartesian coordinates
  95  * are calculated as in Allen & Tildesley (pp. 330-332). Factors factor_phi_*  are coming from the
  96  * derivatives of the torsion angle (phi) with respect to the beads ai, aj, ak, al, (four) coordinates
  97  * and they are multiplied in the force computations with the particle distance
  98  * stored in parameters delta_ante, delta_crnt, delta_post.
  99  *
 100  *  \param[in]  type                             type of force parameters
 101  *  \param[in]  forceparams                      array of parameters for force computations
 102  *  \param[in]  delta_ante                       distance between the first two particles
 103  *  \param[in]  delta_crnt                       distance between the middle pair of particles
 104  *  \param[in]  delta_post                       distance between the last two particles
 105  *  \param[out] factor_phi_ai_ante               force factor for particle ai multiplied with delta_ante
 106  *  \param[out] factor_phi_ai_crnt               force factor for particle ai multiplied with delta_crnt
 107  *  \param[out] factor_phi_ai_post               force factor for particle ai multiplied with delta_post
 108  *  \param[out] factor_phi_aj_ante               force factor for particle aj multiplied with delta_ante
 109  *  \param[out] factor_phi_aj_crnt               force factor for particle aj multiplied with delta_crnt
 110  *  \param[out] factor_phi_aj_post               force factor for particle aj multiplied with delta_post
 111  *  \param[out] factor_phi_ak_ante               force factor for particle ak multiplied with delta_ante
 112  *  \param[out] factor_phi_ak_crnt               force factor for particle ak multiplied with delta_crnt
 113  *  \param[out] factor_phi_ak_post               force factor for particle ak multiplied with delta_post
 114  *  \param[out] factor_phi_al_ante               force factor for particle al multiplied with delta_ante
 115  *  \param[out] factor_phi_al_crnt               force factor for particle al multiplied with delta_crnt
 116  *  \param[out] factor_phi_al_post               force factor for particle al multiplied with delta_post
 117  *  \param[out] prefactor_phi                    multiplication constant of the torsion force
 118  *  \param[out] v                                contribution to energy  (see formula above)
 119  */
 120
 121 void compute_factors_restrdihs(int type,  const t_iparams forceparams[],
 122                                rvec delta_ante, rvec delta_crnt, rvec delta_post,
 123                                real *factor_phi_ai_ante, real *factor_phi_ai_crnt, real *factor_phi_ai_post,
 124                                real *factor_phi_aj_ante, real *factor_phi_aj_crnt, real *factor_phi_aj_post,
 125                                real *factor_phi_ak_ante, real *factor_phi_ak_crnt, real *factor_phi_ak_post,
 126                                real *factor_phi_al_ante, real *factor_phi_al_crnt, real *factor_phi_al_post,
 127                                real *prefactor_phi, real *v);
 128
 129 /*! \brief Compute factors for combined bending-torsion (CBT) potentials.
 130  *
 131  * The combined bending-torsion potential goes to zero in a very smooth manner, eliminating the numerical
 132  * instabilities, when three coarse-grained particles align and the dihedral angle and standard
 133  * dihedral potentials cannot be calculated. The CBT potential is calculated using the formula:
 134  * \f[V_{\rm CBT}(\theta_{i-1}, \theta_i, \phi_i) = k_{\phi} \sin^3\theta_{i-1} \sin^3\theta_{i}
 135  * \sum_{n=0}^4 { a_n \cos^n\phi_i}\f] (see section "Proper dihedrals: Combined bending-torsion potential" from the manual).
 136  * It contains in its expression not only the dihedral angle \f$\phi\f$
 137  * but also \f$\theta_{i-1}\f$ (denoted as theta_ante below) and \f$\theta_{i}\f$ (denoted as theta_post below)
 138  * --- the adjacent bending angles. The derivative of the CBT potential is calculated as:
 139  * \f[\frac{\partial V_{\rm CBT}(\theta_{i-1},\theta_i,\phi_i)} {\partial \vec r_{l}} =  \frac{\partial V_
 140  * {\rm CBT}}{\partial \theta_{i-1}} \frac{\partial \theta_{i-1}}{\partial \vec r_{l}} +
 141  * \frac{\partial V_{\rm CBT}}{\partial \phi_{i    }} \frac{\partial \phi_{i    }}{\partial \vec r_{l}}\f]
 142  * where all the derivatives of the angles with respect to Cartesian coordinates are calculated as
 143  * in Allen & Tildesley (pp. 330-332). Factors f_phi_* come from  the derivatives of the torsion angle
 144  * with respect to the beads ai, aj, ak, al (four) coordinates; f_theta_ante_* come from the derivatives of
 145  * the bending angle theta_ante (theta_{i-1} in formula above) with respect to the beads ai, aj, ak (three
 146  * particles) coordinates and f_theta_post_* come from the derivatives of  the bending angle theta_post
 147  * (theta_{i} in formula above) with respect to the beads aj, ak, al (three particles) coordinates.
 148  *
 149  *  \param[in]  type                             type of force parameters
 150  *  \param[in]  forceparams                      array of parameters for force computations
 151  *  \param[in]  delta_ante                       distance between the first two particles
 152  *  \param[in]  delta_crnt                       distance between the middle pair of particles
 153  *  \param[in]  delta_post                       distance between the last two particles
 154  *  \param[out]  f_phi_ai                        force for particle ai due to derivative in phi angle
 155  *  \param[out]  f_phi_aj                        force for particle aj due to derivative in phi angle
 156  *  \param[out]  f_phi_ak                        force for particle ak due to derivative in phi angle
 157  *  \param[out]  f_phi_al                        force for particle al due to derivative in phi angle
 158  *  \param[out]  f_theta_ante_ai                 force for particle ai due to derivative in theta_ante angle
 159  *  \param[out]  f_theta_ante_aj                 force for particle aj due to derivative in theta_ante angle
 160  *  \param[out]  f_theta_ante_ak                 force for particle ak due to derivative in theta_ante angle
 161  *  \param[out]  f_theta_post_aj                 force for particle aj due to derivative in theta_post angle
 162  *  \param[out]  f_theta_post_ak                 force for particle ak due to derivative in theta_post angle
 163  *  \param[out]  f_theta_post_al                 force for particle al due to derivative in theta_psot angle
 164  *  \param[out] v                                contribution to energy (see formula above)
 165  */
 166
 167 void compute_factors_cbtdihs(int type,  const t_iparams forceparams[],
 168                              rvec delta_ante, rvec delta_crnt, rvec delta_post,
 169                              rvec f_phi_ai, rvec f_phi_aj, rvec f_phi_ak, rvec f_phi_al,
 170                              rvec f_theta_ante_ai, rvec f_theta_ante_aj, rvec f_theta_ante_ak,
 171                              rvec f_theta_post_aj, rvec f_theta_post_ak, rvec f_theta_post_al,
 172                              real * v);
 173
 174 #endif