colvar::rmsd Class Reference

Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*)). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::rmsd:

List of all members.

Public Member Functions
	rmsd (std::string const &conf)
	Constructor.
virtual	~rmsd ()
virtual void	calc_value ()
	Calculate the variable.
virtual void	calc_gradients ()
	Calculate the atomic gradients, to be reused later in order to apply forces.
virtual void	calc_force_invgrads ()
	Calculate the total force from the system using the inverse atomic gradients.
virtual void	calc_Jacobian_derivative ()
	Calculate the divergence of the inverse atomic gradients.
virtual void	apply_force (colvarvalue const &force)
	Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function).
virtual cvm::real	dist2 (colvarvalue const &x1, colvarvalue const &x2) const
	Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue	dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue	dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual cvm::real	compare (colvarvalue const &x1, colvarvalue const &x2) const
	Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error.
Protected Attributes
cvm::real	ref_pos_sum2
	Sum of the squares of ref_coords.

---

Detailed Description

Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*)).

Definition at line 901 of file colvarcomp.h.

---

Constructor & Destructor Documentation

colvar::rmsd::rmsd (  std::string const &  conf  )

Constructor. Definition at line 534 of file colvarcomp_distances.C. References colvarvalue::norm2(), ref_pos_sum2, and colvarvalue::type(). : orientation (conf) { // TODO: refuse to start if hideJacobian is on b_inverse_gradients = true; b_Jacobian_derivative = true; function_type = "rmsd"; x.type (colvarvalue::type_scalar); ref_pos_sum2 = 0.0; for (size_t i = 0; i < ref_pos.size(); i++) { ref_pos_sum2 += ref_pos[i].norm2(); } }

virtual colvar::rmsd::~rmsd (   )  [inline, virtual]

Definition at line 913 of file colvarcomp.h. {}

---

Member Function Documentation

void colvar::rmsd::apply_force (  colvarvalue const &  force  )  [virtual]

Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function). Note: multiple calls to this function within the same simulation step will add the forces altogether Parameters: cvforce  The collective variable force, usually coming from the biases and eventually manipulated by the parent object Reimplemented from colvar::orientation. Definition at line 585 of file colvarcomp_distances.C. References colvarmodule::atom_group::apply_colvar_force(), colvarmodule::atom_group::noforce, and colvarvalue::real_value. { if (!atoms.noforce) atoms.apply_colvar_force (force.real_value); }

void colvar::rmsd::calc_force_invgrads (   )  [virtual]

Calculate the total force from the system using the inverse atomic gradients. Reimplemented from colvar::cvc. Definition at line 592 of file colvarcomp_distances.C. References colvarmodule::atom_group::read_system_forces(), colvarvalue::real_value, and colvarmodule::atom_group::system_force(). { atoms.read_system_forces(); ft.real_value = 0.0; // Note: gradient square norm is 1/N_atoms for (size_t ia = 0; ia < atoms.size(); ia++) { ft.real_value += atoms[ia].grad * atoms[ia].system_force; } ft.real_value *= atoms.size(); }

void colvar::rmsd::calc_gradients (   )  [virtual]

Calculate the atomic gradients, to be reused later in order to apply forces. Reimplemented from colvar::orientation. Definition at line 572 of file colvarcomp_distances.C. References colvarmodule::rotation::q, colvarmodule::real, colvarvalue::real_value, and colvarmodule::quaternion::rotate(). { cvm::real const drmsddx2 = (x.real_value > 0.0) ? 0.5 / (x.real_value * cvm::real (atoms.size())) : 0.0; for (size_t ia = 0; ia < atoms.size(); ia++) { atoms[ia].grad = (drmsddx2 * 2.0 * (atoms[ia].pos - atoms_cog - rot.q.rotate (ref_pos[ia]))); } }

void colvar::rmsd::calc_Jacobian_derivative (   )  [virtual]

Calculate the divergence of the inverse atomic gradients. Reimplemented from colvar::cvc. Definition at line 606 of file colvarcomp_distances.C. References colvarmodule::atom_pos, colvarmodule::rotation::dQ0_2, j, colvarmodule::rotation::q, and colvarvalue::real_value. { // divergence of the back-rotated target coordinates cvm::real divergence = 0.0; // gradient of the rotation matrix cvm::matrix2d <cvm::rvector, 3, 3> grad_rot_mat; // gradients of products of 2 quaternion components cvm::rvector g11, g22, g33, g01, g02, g03, g12, g13, g23; for (size_t ia = 0; ia < atoms.size(); ia++) { // Gradient of optimal quaternion wrt current Cartesian position cvm::vector1d< cvm::rvector, 4 > &dq = rot.dQ0_2[ia]; g11 = 2.0 * (rot.q)[1]*dq[1]; g22 = 2.0 * (rot.q)[2]*dq[2]; g33 = 2.0 * (rot.q)[3]*dq[3]; g01 = (rot.q)[0]*dq[1] + (rot.q)[1]*dq[0]; g02 = (rot.q)[0]*dq[2] + (rot.q)[2]*dq[0]; g03 = (rot.q)[0]*dq[3] + (rot.q)[3]*dq[0]; g12 = (rot.q)[1]*dq[2] + (rot.q)[2]*dq[1]; g13 = (rot.q)[1]*dq[3] + (rot.q)[3]*dq[1]; g23 = (rot.q)[2]*dq[3] + (rot.q)[3]*dq[2]; // Gradient of the rotation matrix wrt current Cartesian position grad_rot_mat[0][0] = -2.0 * (g22 + g33); grad_rot_mat[1][0] = 2.0 * (g12 + g03); grad_rot_mat[2][0] = 2.0 * (g13 - g02); grad_rot_mat[0][1] = 2.0 * (g12 - g03); grad_rot_mat[1][1] = -2.0 * (g11 + g33); grad_rot_mat[2][1] = 2.0 * (g01 + g23); grad_rot_mat[0][2] = 2.0 * (g02 + g13); grad_rot_mat[1][2] = 2.0 * (g23 - g01); grad_rot_mat[2][2] = -2.0 * (g11 + g22); cvm::atom_pos &y = ref_pos[ia]; for (size_t i = 0; i < 3; i++) { for (size_t j = 0; j < 3; j++) { divergence += grad_rot_mat[i][j][i] * y[j]; } } } jd.real_value = x.real_value > 0.0 ? (3.0 * atoms.size() - 4.0 - divergence) / x.real_value : 0.0; }

void colvar::rmsd::calc_value (   )  [virtual]

Calculate the variable. Reimplemented from colvar::orientation. Definition at line 551 of file colvarcomp_distances.C. References colvarmodule::rotation::calc_optimal_rotation(), colvarmodule::atom_group::center_of_geometry(), colvarmodule::rotation::lambda, colvarmodule::atom_group::positions_shifted(), colvarmodule::atom_group::read_positions(), colvarmodule::real, colvarvalue::real_value, ref_pos_sum2, and colvarmodule::atom_group::reset_atoms_data(). { atoms.reset_atoms_data(); atoms.read_positions(); atoms_cog = atoms.center_of_geometry(); rot.calc_optimal_rotation (ref_pos, atoms.positions_shifted (-1.0 * atoms_cog)); cvm::real group_pos_sum2 = 0.0; for (size_t i = 0; i < atoms.size(); i++) { group_pos_sum2 += (atoms[i].pos - atoms_cog).norm2(); } // value of the RMSD (Coutsias et al) cvm::real const MSD = 1.0/(cvm::real (atoms.size())) * ( group_pos_sum2 + ref_pos_sum2 - 2.0 * rot.lambda ); x.real_value = (MSD > 0.0) ? ::sqrt (MSD) : 0.0; }

virtual cvm::real colvar::rmsd::compare (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error. Reimplemented from colvar::orientation.

virtual cvm::real colvar::rmsd::dist2 (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities). colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object. If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients. If constraints are present (and not already implemented by any of the types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface. Finally, another useful application, if you are performing very many operations with these functions, could be to override the member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar type. Reimplemented from colvar::orientation.

virtual colvarvalue colvar::rmsd::dist2_lgrad (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). Reimplemented from colvar::orientation.

virtual colvarvalue colvar::rmsd::dist2_rgrad (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). Reimplemented from colvar::orientation.

---

Member Data Documentation

cvm::real colvar::rmsd::ref_pos_sum2 [protected]

Sum of the squares of ref_coords. Definition at line 907 of file colvarcomp.h. Referenced by calc_value(), and rmsd().

---

The documentation for this class was generated from the following files:

• colvarcomp.h
• colvarcomp_distances.C

---