ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.
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ProtoMol::PAR::Nonbonded Struct Reference

This structure holds data for a nonbonded - including.

#include <PAR.h>

List of all members.

Public Member Functions

 Nonbonded ()
 Nonbonded (int a, std::string b, Real c, Real d, Real e, bool f, bool g, Real h, Real i, Real j, bool k)

Public Attributes

int number
std::string atom
Real polarizability
Real epsilon
Real sigma
bool negative
bool vdw
Real polarizability2
Real epsilon14
Real sigma14
bool negative2

Static Public Attributes

const Real SIGMA_CHARMM19_TO_CHARMM28
const Real SIGMA_CHARMM28_TO_CHARMM19

Friends

Report::MyStreamer & operator<< (Report::MyStreamer &OS, const Nonbonded &p)

Constructor & Destructor Documentation

ProtoMol::PAR::Nonbonded::Nonbonded (   )  [inline]
 

ProtoMol::PAR::Nonbonded::Nonbonded (  int  a,
std::string  b,
Real  c,
Real  d,
Real  e,
bool  f,
bool  g,
Real  h,
Real  i,
Real  j,
bool  k
)  [inline]
 

Friends And Related Function Documentation

Report::MyStreamer& operator<< (  Report::MyStreamer &  OS,
const Nonbonded &  p
)  [friend]
 

Member Data Documentation

std::string ProtoMol::PAR::Nonbonded::atom
 

atom number

Real ProtoMol::PAR::Nonbonded::epsilon
 

well depth or number of effective electrons (see description of negative below)

Real ProtoMol::PAR::Nonbonded::epsilon14
 

VDW parameter well depth or number of effective electrons (see above).

bool ProtoMol::PAR::Nonbonded::negative
 

flag for if the second term is negative - if so, second_term = epsilon or well-depth and the first term is ignored, otherwise second_term = number of effective electrons and the first term is the polarizability default to true

bool ProtoMol::PAR::Nonbonded::negative2
 

flag for a negative VDW paramenter second term (see above), default to true

int ProtoMol::PAR::Nonbonded::number
 

nonbonded number

Real ProtoMol::PAR::Nonbonded::polarizability
 

polarizability or ignore (see description of negative below), default to zero

Real ProtoMol::PAR::Nonbonded::polarizability2
 

VDW parameter polarizability, default to zero.

Real ProtoMol::PAR::Nonbonded::sigma
 

minimum radius divided by 2

Real ProtoMol::PAR::Nonbonded::sigma14
 

VDW parameter minimum radius divided by 2.

const Real ProtoMol::PAR::Nonbonded::SIGMA_CHARMM19_TO_CHARMM28 [static]
 

const Real ProtoMol::PAR::Nonbonded::SIGMA_CHARMM28_TO_CHARMM19 [static]
 

bool ProtoMol::PAR::Nonbonded::vdw
 

default to true - likely there will be epsilon 1:4 and sigma 1:4, flag to see if there is a second set, indicating VDW parameters

The documentation for this struct was generated from the following files: Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.