SSAGES::RMSDCV Class Reference

Collective variable to calculate root mean square displacement. More...

#include <RMSDCV.h>

Inheritance diagram for SSAGES::RMSDCV:

Public Member Functions
	RMSDCV (std::vector< int > atomids, std::string molxyz, bool use_range=false)
	Constructor. More...
void	Initialize (const Snapshot &snapshot) override
void	Evaluate (const Snapshot &snapshot) override
Public Member Functions inherited from SSAGES::CollectiveVariable
	CollectiveVariable ()
	Constructor.
double	GetValue () const
	Get current value of the CV. More...
virtual double	GetMinimumImage (double) const
	Returns the minimum image of a CV based on the input location. More...
virtual double	GetPeriodicValue (double location) const
	Apply periodic boundaries to a given value. More...
const std::vector< Vector3 > &	GetGradient () const
	Get current gradient of the CV. More...
const Matrix3 &	GetBoxGradient () const
	Get gradient contribution to box.
const std::array< double, 2 > &	GetBoundaries ()
	Get CV boundaries. More...
virtual double	GetDifference (double location) const

Private Attributes
std::vector< int >	atomids_
	IDs of the atoms used for Rg calculation.
std::vector< int >	pertatoms_
	Array to store indicies of atoms of interest.
std::string	molecule_
	Name of model structure.
std::vector< Vector3 >	refcoord_
	Store reference structure coordinates.
Vector3	COMref_
	Center of mass of reference.

Additional Inherited Members
Static Public Member Functions inherited from SSAGES::CollectiveVariable
static CollectiveVariable *	BuildCV (const Json::Value &json, const std::string &path)
	Set up collective variable. More...
Protected Attributes inherited from SSAGES::CollectiveVariable
std::vector< Vector3 >	grad_
	Gradient vector dCv/dxi.
Matrix3	boxgrad_
	Gradient w.r.t box vectors dCv/dHij.
double	val_
	Current value of CV.
std::array< double, 2 >	bounds_
	Bounds on CV.

Detailed Description

Collective variable to calculate root mean square displacement.

RMSD calculation performed as reported in Coutsias, E. A., Seok, C., and Dill, K. A., "Using Quaternions to Calculate RMSD", J. Comput. Chem. 25: 1849-1857, 2004

Definition at line 39 of file RMSDCV.h.

Constructor & Destructor Documentation

SSAGES::RMSDCV::RMSDCV ( std::vector< int >  atomids, std::string  molxyz, bool  use_range = false  )

inline

Constructor.

Parameters

atomids	IDs of the atoms defining Rg.
molxyz	String determining the molecule.
use_range	If True Use range of atoms defined by the two atoms in atomids.

Construct a RMSD CV.

Todo:

Bounds needs to be an input and periodic boundary conditions

Definition at line 67 of file RMSDCV.h.

References atomids_.

                                                                                 :
        atomids_(atomids), molecule_(molxyz)
        {
            if(use_range)
            {
                if(atomids.size() != 2)
                {   std::cout<<"RMSDCV: If using range, must define only two atoms!"<<std::endl;
                    exit(0);
                }

                atomids_.clear();

                if(atomids[0] >= atomids[1])
                {   std::cout<<"RMSDCV: Please reverse atom range or check that atom range is not equal!"<<std::endl;
                    exit(0);
                }                   
                for(int i = atomids[0]; i <= atomids[1];i++)
                    atomids_.push_back(i);
            }
        }

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

• /home/cody/SSAGES/src/CVs/RMSDCV.h