anonymous_namespace{position_restraints.cpp} Namespace Reference

Functions
void	posres_dx (const rvec x, const rvec pos0A, const rvec pos0B, const gmx::RVec &centerOfMassAScaled, const gmx::RVec &centerOfMassBScaled, real lambda, const t_pbc &pbc, RefCoordScaling refcoord_scaling, int npbcdim, rvec dx, rvec rdist, rvec dpdl)
	returns dx, rdist, and dpdl for functions posres() and fbposres()
real	do_fbposres_cylinder (int fbdim, rvec fm, rvec dx, real rfb, real kk, gmx_bool bInvert)
	Computes forces and potential for flat-bottom cylindrical restraints. Returns the flat-bottom potential.
real	fbposres (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec4 *forces, gmx::RVec *virial, const t_pbc &pbc, RefCoordScaling refcoord_scaling, PbcType pbcType, const gmx::ArrayRef< const gmx::RVec > centersOfMass, const gmx::ArrayRef< const unsigned short > refScaleComIndices, gmx::ArrayRef< gmx::RVec > centersOfMassScaled)
	Compute energies and forces for flat-bottomed position restraints. More...
template<bool computeForce>
real	posres (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec4 *forces, gmx::RVec *virial, const struct t_pbc &pbc, real lambda, real *dvdlambda, RefCoordScaling refcoord_scaling, const gmx::ArrayRef< const gmx::RVec > centersOfMassA, const gmx::ArrayRef< const gmx::RVec > centersOfMassB, const gmx::ArrayRef< const unsigned short > refScaleComIndices, gmx::ArrayRef< gmx::RVec > centersOfMassAScaled, gmx::ArrayRef< gmx::RVec > centersOfMassBScaled)
	Compute energies and forces, when requested, for position restraints. More...

Function Documentation

real anonymous_namespace{position_restraints.cpp}::fbposres	(	int	nbonds,
		const t_iatom	forceatoms[],
		const t_iparams	forceparams[],
		const rvec	x[],
		rvec4 *	forces,
		gmx::RVec *	virial,
		const t_pbc &	pbc,
		RefCoordScaling	refcoord_scaling,
		PbcType	pbcType,
		const gmx::ArrayRef< const gmx::RVec >	centersOfMass,
		const gmx::ArrayRef< const unsigned short >	refScaleComIndices,
		gmx::ArrayRef< gmx::RVec >	centersOfMassScaled
	)

Compute energies and forces for flat-bottomed position restraints.

Returns the flat-bottomed potential. Same PBC treatment as in normal position restraints

template<bool computeForce>

real anonymous_namespace{position_restraints.cpp}::posres	(	int	nbonds,
		const t_iatom	forceatoms[],
		const t_iparams	forceparams[],
		const rvec	x[],
		rvec4 *	forces,
		gmx::RVec *	virial,
		const struct t_pbc &	pbc,
		real	lambda,
		real *	dvdlambda,
		RefCoordScaling	refcoord_scaling,
		const gmx::ArrayRef< const gmx::RVec >	centersOfMassA,
		const gmx::ArrayRef< const gmx::RVec >	centersOfMassB,
		const gmx::ArrayRef< const unsigned short >	refScaleComIndices,
		gmx::ArrayRef< gmx::RVec >	centersOfMassAScaled,
		gmx::ArrayRef< gmx::RVec >	centersOfMassBScaled
	)

Compute energies and forces, when requested, for position restraints.

Note that position restraints require a different pbc treatment from other bondeds