\brief Communication between colvars and VMD (implementation of \link colvarproxy \endlink)

\brief Collective variables module (main class) Class to control the collective variables calculation. An object (usually one) of this class is spaw

\brief Communication between colvars and NAMD (implementation of \link colvarproxy \endlink)

Class holding the trajectory of a collective variable. The series of step numbers are included as well, because collective variables may

Trajectories of collective variables, as read from a list of colvars.traj files. Can be accessed as a dictionary using a variable's name as ke

Free energy gradients class

struct for packed data communication of coordinates and forces. */

\brief Colvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of Ca-Ca-Ca angles and hydrogen bonds

\brief Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI])

\brief Colvar component: flat vector of Cartesian coordinates Mostly useful to compute scripted colvar values

\brief Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2])

\brief Colvar component: dihedPC Projection of the config onto a dihedral principal component See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007)

\brief Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI])

\brief Colvar component: angle between the dipole of a molecule and an axis formed by two groups of atoms(colvarvalue::type_scalar type, range [0:PI])

\brief Colvar component: dipole magnitude of a molecule

\brief Colvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unit3vector type, range [-1:1]x[-1:

\brief Colvar component: average distance between two groups of atoms, weighted as the sixth power, as in NMR refinements(colvarvalue::type_scalar typ

\brief Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component)

\brief Colvar component: distance vector between centers of mass of two groups (\link colvarvalue::type_3vector \endlink type, range (-*:*)x(-*:*)x(-*

\brief Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*))

\brief Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*))

\brief Colvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-*:*))

\brief Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2])

\brief Colvar component: alternative path collective variable using geometry, variable s For more information see https://plumed.github.io/doc-v2.5/us

\brief Colvar component: alternative path collective variable using geometry, variable s Allow any combination of existing (scalar) CVs For more infor

\brief Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*))

\brief Colvar component: alternative path collective variable using geometry, variable z This should be merged with gspath in the same class by class

\brief Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type

\brief Colvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*))

\brief Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*))

Current only linear combination of sub-CVCs is available

\brief Colvar component: total value of a scalar map (usually implemented as a grid by the simulation engine)

\brief Colvar component: orientation in space of an atom group, with respect to a set of reference coordinates (colvarvalue::type_quaternion type, ran

\brief Colvar component: angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [0:PI))

\brief Colvar component: cosine of the angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [-1:1])

\brief Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180])

\brief Colvar component: polar coordinate theta of a group (colvarvalue::type_scalar type, range [0:180])

\brief Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses \link colvar::orientation \

\brief Colvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2])

\brief Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI])

\brief Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1])

\brief Colvar_grid derived class to hold counters in discrete n-dim colvar space

Class for accumulating the gradient of a scalar function on a grid