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t_mdatoms Struct Reference

#include <gromacs/mdtypes/mdatom.h>

Description

Declares mdatom data structure.

Public Attributes

real tmassA
 Total mass in state A.
 
real tmassB
 Total mass in state B.
 
real tmass
 Total mass.
 
int nr
 Number of atoms in arrays.
 
int nalloc
 Number of elements in arrays.
 
int nenergrp
 Number of energy groups.
 
gmx_bool bVCMgrps
 Do we have multiple center of mass motion removal groups.
 
int nPerturbed
 Number of perturbed atoms.
 
int nMassPerturbed
 Number of atoms for which the mass is perturbed.
 
int nChargePerturbed
 Number of atoms for which the charge is perturbed.
 
int nTypePerturbed
 Number of atoms for which the type is perturbed.
 
gmx_bool bOrires
 Do we have orientation restraints.
 
realmassA
 Atomic mass in A state.
 
realmassB
 Atomic mass in B state.
 
realmassT
 Atomic mass in present state.
 
realinvmass
 Inverse atomic mass.
 
realchargeA
 Atomic charge in A state.
 
realchargeB
 Atomic charge in B state.
 
realsqrt_c6A
 Dispersion constant C6 in A state.
 
realsqrt_c6B
 Dispersion constant C6 in A state.
 
realsigmaA
 Van der Waals radius sigma in the A state.
 
realsigmaB
 Van der Waals radius sigma in the B state.
 
realsigma3A
 Van der Waals radius sigma^3 in the A state.
 
realsigma3B
 Van der Waals radius sigma^3 in the B state.
 
gmx_boolbPerturbed
 Is this atom perturbed.
 
int * typeA
 Type of atom in the A state.
 
int * typeB
 Type of atom in the B state.
 
unsigned short * ptype
 Particle type.
 
unsigned short * cTC
 Group index for temperature coupling.
 
unsigned short * cENER
 Group index for energy matrix.
 
unsigned short * cACC
 Group index for acceleration.
 
unsigned short * cFREEZE
 Group index for freezing.
 
unsigned short * cVCM
 Group index for center of mass motion removal.
 
unsigned short * cU1
 Group index for user 1.
 
unsigned short * cU2
 Group index for user 2.
 
unsigned short * cORF
 Group index for orientation restraints.
 
gmx_boolbQM
 QMMM atoms.
 
int homenr
 Number of atoms on this processor. TODO is this still used?
 
real lambda
 The lambda value used to create the contents of the struct.
 

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