Index

Symbols

: Ewald optimisation

A

algorithm, [1], [2] FIQA, [1] integration NOSQUISH, [1], [2] RATTLE, [1], [2], [3], [4] SHAKE, [1], [2], [3], [4], [5], [6] Verlet, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] Verlet neighbour list, [1]

AMBER force field, [1] angular momentum angular restraints atomic stress

B

barostat, [1], [2], [3] Berendsen Nosé-Hoover, [1], [2]

boundary conditions, [1], [2] cubic

C

CCP5 constraints bond, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] bonds, [1] Gaussian, [1], [2], [3], [4], [5], [6] PMF, [1], [2], [3], [4], [5] see bond

constraints!bond

D

dependent dielectric direct Coulomb sum, [1], [2] distance dependant dielectric, [1] distance restraints, [1]

DL_POLY_5 software licence dlpoly2 DPD Dreiding force field

E

ensemble, [1] Andersen NVT Anderson NVT Berendsen N$sigma$T, [1] Berendsen NPT, [1] Berendsen NVT, [1] canonical DPD NVT Evans NVT, [1] Gentle Stochastic NVT Inhomogeneous Langevin NVT, [1] Langevin N$simga$T Langevin NPT, [1] Langevin NVT, [1] Langevin N|sigma|T Martyna-Tuckerman-Klein N$sigma$T, [1] Martyna-Tuckerman-Klein NPT, [1] Nosé-Hoover N$sigma$T, [1] Nosé-Hoover NPT Nosé-Hoover NVT, [1], [2] NVE, [1], [2]

equations of motion Euler, [1] rigid body error messages, [1] Ewald optimisation SPME, [1] summation, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]

F

force field, [1], [2], [3], [4], [5], [6], [7], [8], [9] AMBER, [1], [2] DL_POLY, [1] Dreiding, [1], [2], [3] GROMOS, [1]

force-shifted Coulomb sum FORTRAN90, [1], [2], [3], [4], [5], [6], [7], [8], [9]

G

Gaussian constraints, [1], [2], [3], [4], [5]

GROMOS force field, [1] GUI, [1], [2], [3]

I

integration algorithm

inversional restraints

J

Java GUI

L

licence long-ranged corrections metal van der Waals

M

minimisation conjugate gradients programmed zero temperature

multipolar electrostatics

N

non-bonded potential

P

parallelisation, [1], [2] Domain Decomposition intramolecular terms, [1] polarisation, [1] shell model, [1], [2], [3], [4], [5], [6], [7], [8] shell models potentail four-body potential 2BEAM 2BEEAM bond, [1], [2], [3], [4], [5], [6], [7], [8] bonded, [1] calcite, [1] chemical bond, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] dihedral, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] diheral EAM EEAM, [1] electrostatics, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] external field, [1], [2], [3] external fields four-body, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] improper dihedral, [1], [2], [3], [4], [5] intermolecular intramolecular, [1], [2] inversion, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] metal, [1], [2], [3], [4], [5], [6], [7], [8], [9] non-bonded, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] tabulated, [1], [2] Tersoff, [1], [2], [3], [4], [5], [6], [7], [8], [9] tether, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] tethered three-body, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] valence angle, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] van der Waals, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]

potetial EAM

Q

quaternions

R

reaction field, [1]

rigid body, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] rigid bond, [1]

S

stress stress tensor, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25] sub-directory, [1], [2], [3], [4], [5], [6], [7], [8] bench build, [1] cmake, [1] data, [1] execute, [1] java, [1] manual source, [1] utility, [1] utils, [1]

summation Ewald, [1], [2], [3]

T

thermostat, [1], [2], [3], [4] Nosé-Hoover, [1] torsional restraints Two-Temperature Model, [1], [2], [3], [4], [5], [6], [7] boundary conditions, [1] electron-phonon coupling, [1] electronic stopping energy deposition Explicit finite-difference scheme heat capacity Heat diffusion laser excitation swift heavy ions thermal conductivity thermal diffusivity

U

units DL_POLY, [1] energy pressure, [1], [2], [3], [4]

user registration

V

Verlet algorithm

Verlet neighbour Verlet neighbour list, [1], [2]

W

WWW, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16]