mstk.forcefield.OplsDihedralTerm

class mstk.forcefield.OplsDihedralTerm(type1, type2, type3, type4, k1, k2, k3, k4)

Dihedral term in OPLS form

The energy function is

>>> U = k_1*(1+cos(phi)) + k_2*(1-cos(2*phi)) + k_3*(1+cos(3*phi)) - k_4*(1-cos(4*phi))

OPLS form is commonly used, therefore we don’t generalize it with PeriodicDihedralTerm.

During the initialization, the sequence of atom types to use i-j-k-l or l-k-j-i will be determined by their string order.

DihedralTerm allows wildcard(*) for side atoms. For sorting purpose, the wildcard will always be the last. During force field matching, the terms with wildcard will have lower priority. The terms with wildcard will be used only if exact match cannot be found.

Parameters:

• type1 (str) –

• type2 (str) –

• type3 (str) –

• type4 (str) –

• k1 (float) –

• k2 (float) –

• k3 (float) –

• k4 (float) –

type1

Type:

str

type2

Type:

str

type3

Type:

str

type4

Type:

str

k1

Type:

float

k2

Type:

float

k3

Type:

float

k4

Type:

float

Methods

__init__(type1, type2, type3, type4, k1, k2, ...)
evaluate_energy(val)	Evaluate the energy for a force field term like HarmonicBondTerm, PeriodicDihedralTerm, etc...
get_alias()	Return a short alias for the name of this class
to_periodic_term()	Get the equivalent PeriodicDihedralTerm
to_zff()	Pack the attributes of a term into a string so that can be saved into a line in ZFF file.
to_zff_header()	Header string to explain a line in ZFF format
to_zfp()	Pack the attributes of a term into a dict so that can be saved into ZFP xml file.

Attributes

is_zero	Whether or not this dihedral terms always give zero energy.
name	The name of this force field term.

evaluate_energy(val)

Evaluate the energy for a force field term like HarmonicBondTerm, PeriodicDihedralTerm, etc…

It is mainly for debugging. It is not (and can not be) implemented for all terms.

Parameters:

val (float) – The value of distance, angle, dihedral or improper.

Returns:

energy

Return type:

float

property is_zero

Whether or not this dihedral terms always give zero energy.

For linear groups like alkyne and nitrile, dihedral terms are presented in topology. But the parameters for these terms usually equal to zero.

Returns:

is

Return type:

bool

to_periodic_term()

Get the equivalent PeriodicDihedralTerm

Returns:

term

Return type:

PeriodicDihedralTerm