Augmenting High-Performance Mobile Cloud Computations for Big Data in AMBER

Table 2

Parameters required to calculate bond stretch terms and angle bend terms.

Sr. No.	Parameter	Description
(1)	“forceConstant”	Constant variable used in calculation
(2)	“equilibrium distance.”	Distance between two atoms
(3)	“angleBendTerms [ix5]”	All the four values of angle bend terms according to functional form
(4)	“coordinates [atomix3]”	, , coordinates of atom stored in array
(5)	“dihedralAngleTerms [ix7]”	All the four values of dihedral angle terms according to functional form
(6)	“coordinates [atomix3]”	, , coordinates of atom stored in array
(7)	“coordinates [atomix3]”	, , coordinates of atom stored in array
(8)	“nonBondedTerms [ix4]”	All the four values of nonbonded terms according to functional form
(9)	“coulomb factor.”	It is calculated using permittivity and permittivity scale and a constant value 332
(10)	“coordinates [atomix3]”	, , coordinates of atom stored in array
(11)	“bond length.”	The natural bond length
(12)	“energy”	The partial value of energy due to bond stretch terms is calculated and stored in it
(13)	“angleBendTerms [ix5]”	All the four values of angle bend terms according to functional form
(14)	“coordinates [atomix3]”	, , coordinates of atom stored in array
(15)	“theta deg”	It is calculated in this function from coordinates
(16)	“term”	Intermediate value to calculate energy due to angle bend
(17)	“energy”	The partial value of energy due to angle bend terms is calculated and stored in it