Index

algorithm

no title | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Integration algorithms | The CONTROL File

Brode-Ahlrichs

The DL_POLY_2 Force Field | The Replicated Data Strategy | Distributing the Nonbonded Terms | Distributing the Nonbonded Terms

FIQA

Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration of the Rigid

multiple timestep

The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | Distributing the Nonbonded Terms | Constructing Nonstandard Versions | Constructing Nonstandard Versions | The CONTROL File Directives | The CONTROL File Directives | Further Comments on the | Further Comments on the | Further Comments on the | Simulation Progress | Test Case 1: KNaSi$_2$O$_5$ | Message 153: error - | Message 385: error - | Message 385: error - | Message 386: error - | Message 398: error - | Message 422: error -

QSHAKE

Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | The RD-SHAKE and Parallel

RD-SHAKE

Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Bond Constraints | The RD-SHAKE and Parallel | The RD-SHAKE and Parallel | Message 102: error - | Message 105: error - | Message 190: error -

SHAKE

Molecular Dynamics Algorithms | The Replicated Data Strategy | The RD-SHAKE and Parallel | The RD-SHAKE and Parallel | The RD-SHAKE and Parallel | The RD-SHAKE and Parallel | The Parameters and their | Message 438: error -

Verlet

Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Short Ranged (van der | Atomistic and Charge Group | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Bond Constraints | Bond Constraints | Bond Constraints | Bond Constraints | Bond Constraints | Nosé- Hoover Thermostat | Gaussian Constraints | The Hoover Barostat | The RD-SHAKE and Parallel

AMBER

The DL_POLY Package | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Macromolecules | Macromolecules | Adding Solvent to a

angular restraints

Angular Restraints

barostat

Molecular Dynamics Algorithms | Integration of the Rigid | Integration of the Rigid | The CONTROL File Directives | Message 466: error -

Berendsen

Berendsen Barostat | Linked Rigid Bodies | Test Case 5: Shell

Hoover

The Hoover Barostat | The Hoover Barostat

boundary conditions

Boundary Conditions | Boundary Conditions | Long Ranged Electrostatic (Coulombic) | Constructing Nonstandard Versions | Inorganic Materials | Test Case 3: An | Test Case 5: Shell | Test Case 10: DNA | Introduction | Introduction | Message 67: error - | no title

cubic

Further Comments | Message 67: error - | Message 79: error - | Message 300: error -

hexagonal prism

Further Comments

parallelpiped

Message 67: error - | Message 79: error - | Message 300: error -

rhombic dodecahedron

Further Comments

slab

Message 300: error -

truncated octahedron

Further Comments

CCP5

The DL_POLY Package | The DL_POLY Package | The DL_POLY Package | The DL_POLY Package | The public Sub-directory | Obtaining the Source Code

charge groups

. | Test Case 4: Shell | Message 97: error - | Message 220: error - | Message 230: error -

COMMON blocks

Internal Data Transfer | Internal Data Transfer | FORTRAN Parameters | Modifying the Makefile

constrains

bond

The Parameters and their

constraints

bond

Molecular Systems | Molecular Systems | Molecular Dynamics Algorithms | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Bond Constraints | Bond Constraints | Potential of Mean Force | Potential of Mean Force | Description of Rigid Body | Description of Rigid Body | Description of Rigid Body | Integration of the Rigid | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | The RD-SHAKE and Parallel | The RD-SHAKE and Parallel | The RD-SHAKE and Parallel | The RD-SHAKE and Parallel | Constructing Nonstandard Versions | Constructing Nonstandard Versions | . | . | Simulation Progress | Test Case 3: An | Test Case 7: Linked | Test Case 9: A | The Parameters and their | Message 40: error - | Message 41: error - | Message 70: error - | Message 99: error - | Message 105: error - | Message 432: error -

Gaussian

Ewald Sum | Ewald Sum | Ewald Sum | Ewald Sum | Ewald Sum | Ewald Sum | Thermostats | Test Case 2: Metal

PMF

Potential of Mean Force | Potential of Mean Force | . | .

CVS

Version Control System (CVS) | Version Control System (CVS) | Internal Documentation

direct Coulomb sum

Long Ranged Electrostatic (Coulombic) | Direct Coulomb Sum | Coulomb Sum with Distance

distance dependant dielectric

Coulomb Sum with Distance | Reaction Field | The CONTROL File Directives | Further Comments on the | Message 424: error -

distance restraints

Distance Restraints | Distance Restraints

DLPROTEIN

Macromolecules

ensemble

Molecular Dynamics Algorithms | no title | Message 430: error -

Berendsen N$\sigma$T

The CONTROL File Directives

Berendsen N$\sigma$T

Further Comments on the

Berendsen N$\sigma$T

Further Comments on the

Berendsen N$\sigma$T

Molecular Dynamics Algorithms

Berendsen N$\sigma$T

Molecular Dynamics Algorithms

Berendsen N$\sigma$T

Molecular Dynamics Algorithms

Berendsen N$\sigma$T

Integration algorithms

Berendsen N$\sigma$T

Integration algorithms

Berendsen N$\sigma$T

Integration algorithms

Berendsen NPT

Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Further Comments on the | Further Comments on the

Berendsen NVT

Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | The CONTROL File Directives | The CONTROL File Directives | Further Comments on the | Further Comments on the

BerendsenN$\sigma$T

Integration algorithms

canonical

Thermostats

Evans NVT

Molecular Dynamics Algorithms | Integration algorithms | Integration algorithms | The CONTROL File Directives | Further Comments on the | Further Comments on the

Hoover N$\sigma$T

Further Comments on the

Hoover N$\sigma$T

Molecular Dynamics Algorithms

Hoover N$\sigma$T

Molecular Dynamics Algorithms

Hoover N$\sigma$T

Molecular Dynamics Algorithms

Hoover N$\sigma$T

Integration algorithms

Hoover N$\sigma$T

Integration algorithms

Hoover N$\sigma$T

Integration algorithms

Hoover N$\sigma$T

Integration algorithms

Hoover NPT

Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | The CONTROL File Directives | Further Comments on the

Hoover NVT

Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Integration algorithms | Further Comments on the

microcanonical

see ensemble,NVE

NVE

Thermostats | The CONTROL File Directives | Further Comments on the | Further Comments on the | Further Comments on the

error messages

The DL_POLY_2 Internal Error | Introduction to Message 514: error -

Ewald

Hautman Klein

Long Ranged Electrostatic (Coulombic) | no title | Hautman Klein Ewald Optimisation | The CONTROL File Directives | Slab boundary conditions (IMCON=6)

optimisation

Ewald sum and SPME | Ewald sum and SPME | Ewald sum and SPME

SPME

Required Program Libraries | Long Ranged Electrostatic (Coulombic) | Smoothed Particle Mesh Ewald | Modifying the Makefile | Ewald sum and SPME | The CONTROL File Directives | Test Case 10: DNA

summation

Long Ranged Electrostatic (Coulombic) | Long Ranged Electrostatic (Coulombic) | Atomistic and Charge Group | Ewald Sum | Ewald Sum | Ewald Sum | Ewald Sum | Ewald Sum | Ewald Sum | The DL_POLY_2 Multiple Timestep | The Replicated Data Strategy | Modifications for the Ewald | Ewald sum and SPME | Ewald sum and SPME | Ewald sum and SPME | Ewald sum and SPME | Ewald sum and SPME | The CONTROL File Directives | Further Comments on the | Further Comments on the | Test Case 1: KNaSi$_2$O$_5$ | Test Case 5: Shell | Test Case 9: A | Message 180: error - | Message 185: error - | Message 250: error - | Message 330: error - | Message 433: error -

force field

no title | The DL_POLY_2 Force Field | no title | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Dihedral Angle Potentials | External Fields | External Fields | Adding Solvent to a | Message 12: error - | Message 105: error -

AMBER

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field

DL_POLY

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field to Dynamical Shell Model

Dreiding

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Three Body Potentials | Three Body Potentials | Test Case 9: A | Test Case 10: DNA | Test Case 11: Hautman-Klein

GROMOS

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field

FORTRAN 77

Programming Language | Target Computers | Internal Documentation | Internal Documentation | FORTRAN Parameters | Constructing the Standard Version | Modifying the Makefile | Function

FORTRAN 90

Programming Language | Memory Management | Internal Data Transfer

FTP

The public Sub-directory | Obtaining the Source Code | Obtaining the Source Code | Obtaining the Source Code

Graphical User Interface

The java Sub-directory | A Guide to Preparing | Analysing Results | Definitions of Variables

GROMOS

The DL_POLY Package | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field

Hautman Klein Ewald

see Ewald
Hautman Klein

Java GUI

Java Graphical User Interface | The java Sub-directory

licence

The DL_POLY Package

long range corrections

Sutton-Chen

Metal Potentials

van der Waals

Short Ranged (van der

parallelisation

no title | The Replicated Data Strategy

Ewald summation

Modifications for the Ewald

intramolecular terms

Distributing the Intramolecular Bonded | Distributing the Intramolecular Bonded

Replicated Data

Parallel Algorithms

Verlet neighbour list

Distributing the Nonbonded Terms

polarisation

Dynamical Shell Model | Dynamical Shell Model | Test Case 5: Shell

dynamical shell model

Dynamical Shell Model | Dynamical Shell Model | Dynamical Shell Model | Message 93: error - | Message 97: error -

potential

bond

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Bond Potentials | Bond Potentials | Bond Potentials | Bond Potentials | Distance Restraints | Dihedral Angle Potentials | Improper Dihedral Angle Potentials | Tethering Forces | Three Body Potentials | Dynamical Shell Model | Distributing the Intramolecular Bonded | The RD-SHAKE and Parallel | Inorganic Materials | . | Simulation Progress | The Parameters and their | The Parameters and their | The Parameters and their | The Parameters and their | Message 30: error - | Message 31: error - | Message 444: error -

Coulombic

see potential,electrostatic

dihedral

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Dihedral Angle Potentials | Dihedral Angle Potentials | Dihedral Angle Potentials | Improper Dihedral Angle Potentials | Improper Dihedral Angle Potentials | Improper Dihedral Angle Potentials | Improper Dihedral Angle Potentials | Improper Dihedral Angle Potentials | Inversion Angle Potentials | The Replicated Data Strategy | Distributing the Intramolecular Bonded | . | Simulation Progress | The Parameters and their | The Parameters and their | The Parameters and their | Message 60: error - | Message 61: error - | Message 448: error -

electrostatic

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Units | The DL_POLY_2 Force Field | Distance Restraints | Angular Restraints | no title | Long Ranged Electrostatic (Coulombic) | Atomistic and Charge Group | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The CONTROL File Directives | The CONTROL File Directives | The CONTROL File Directives | The CONTROL File Directives | Further Comments on the | Simulation Progress | Simulation Progress | Test Case 1: KNaSi$_2$O$_5$ | Test Case 3: An | Test Case 9: A | Message 383: error - | Message 424: error - | Message 446: error -

four-body

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The Intermolecular Potential Functions | Four Body Potentials | Four Body Potentials | Four Body Potentials | Four Body Potentials | Four Body Potentials | Four Body Potentials | Four Body Potentials | . | . | . | Simulation Progress | The Parameters and their | The Parameters and their | Message 19: error - | Message 79: error - | Message 89: error - | Message 91: error - | no title | Message 443: error - | Message 453: error -

improper dihedral

The DL_POLY_2 Force Field | Improper Dihedral Angle Potentials | Improper Dihedral Angle Potentials | The Replicated Data Strategy

intramolecular

The Intermolecular Potential Functions | Four Body Potentials | Constructing Nonstandard Versions

inversion

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Four Body Potentials | Four Body Potentials | . | The Parameters and their | The Parameters and their | The Parameters and their | The Parameters and their | no title | Message 449: error -

metal

The DL_POLY_2 Force Field | Metal Potentials | Message 71: error - | Message 71: error - | Message 151: error -

nonbonded

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Distributing the Nonbonded Terms | Distributing the Nonbonded Terms | Three Body Forces | Note on Interpolation Schemes | Note on Interpolation Schemes | Inorganic Materials | Adding Solvent to a | The CONTROL File Directives | Definitions of Variables | . | . | Non-bonded Interactions | Message 13: error - | Message 13: error -

Sutton-Chen

see potential,metal

tabulated

The TABLE File | Message 22: error - | Message 23: error -

tethered

Tethering Forces | Tethering Forces | Tethering Forces | Tethering Forces | Frozen Atoms | . | Simulation Progress | Simulation Progress | Test Case 8: An | The Parameters and their | The Parameters and their | no title | Message 450: error -

three-body

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Valence Angle Potentials | The Intermolecular Potential Functions | Three Body Potentials | Three Body Potentials | Three Body Potentials | Three Body Potentials | Three Body Potentials | Three Body Potentials | Three Body Potentials | Three Body Forces | Inorganic Materials | Inorganic Materials | . | . | . | Simulation Progress | Simulation Progress | The Parameters and their | The Parameters and their | Message 18: error - | Message 69: error - | no title | Message 84: error - | no title | Message 86: error - | Message 451: error -

torsion

see potential,dihedral

valence angle

The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | The DL_POLY_2 Force Field | Valence Angle Potentials | Valence Angle Potentials | Valence Angle Potentials | Inversion Angle Potentials | Three Body Potentials | Three Body Potentials | Three Body Potentials | The Replicated Data Strategy | Three Body Forces | Constructing Nonstandard Versions | Inorganic Materials | . | . | Simulation Progress | The Parameters and their | The Parameters and their | The Parameters and their | The Parameters and their | Message 50: error - | Message 51: error -

van der Waals

The DL_POLY_2 Force Field | Distance Restraints | Angular Restraints | The DL_POLY_2 Multiple Timestep | Constructing Nonstandard Versions | Note on Interpolation Schemes | Further Comments on the | . | The Parameters and their | Message 400: error - | Message 402: error -

quaternions

Molecular Dynamics Algorithms | Integration algorithms | Integration of the Rigid | Integration of the Rigid | The CONTROL File Directives

reaction field

no title | Reaction Field | Reaction Field

reactionfield

The CONTROL File Directives

respa

Molecular Dynamics Algorithms | The respa Sub-directory | The DL_POLY_2 RESPA Multiple

rigid body

Molecular Systems | Molecular Systems | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Molecular Dynamics Algorithms | Frozen Atoms | Integration algorithms | Bond Constraints | Description of Rigid Body | Description of Rigid Body | Integration of the Rigid | Integration of the Rigid | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | Linked Rigid Bodies | The DL_POLY_2 RESPA Multiple | The RD-SHAKE and Parallel | Constructing Nonstandard Versions | Test Case 3: An | Test Case 4: Shell | Test Case 7: Linked | Test Case 9: A | The Parameters and their | The Parameters and their | The Parameters and their | Message 93: error - | Message 301: error - | Message 302: error - | Message 303: error - | Message 304: error - | Message 320: error - | no title | Message 360: error - | Message 430: error - | Message 456: error - | Message 508: error -

rigid bond

see constraints,bond

rigid ion

Molecular Dynamics Algorithms | The DL_POLY_2 RESPA Multiple

rigid molecule

see rigid body

SPME

see Ewald
SPME

stress tensor

Valence Angle Potentials | Valence Angle Potentials | Dihedral Angle Potentials | Dihedral Angle Potentials | Inversion Angle Potentials | Inversion Angle Potentials | Tethering Forces | Tethering Forces | Frozen Atoms | Short Ranged (van der | Short Ranged (van der | Metal Potentials | Three Body Potentials | Four Body Potentials | Direct Coulomb Sum | Direct Coulomb Sum | Truncated and Shifted Coulomb | Truncated and Shifted Coulomb | Coulomb Sum with Distance | Coulomb Sum with Distance | Ewald Sum | Reaction Field | Dynamical Shell Model | Bond Constraints | Bond Constraints | Barostats | Message 434: error - | Message 434: error -

sub-directory

Macros | cleanup | cleanup | copy | select | store | store | store

bench

The DL_POLY_2 Directory Structure

build

The DL_POLY_2 Directory Structure

data

The DL_POLY_2 Directory Structure

execute

The DL_POLY_2 Directory Structure | Message 1: error -

java

The DL_POLY_2 Directory Structure

public

The DL_POLY_2 Directory Structure

respa

The DL_POLY_2 Directory Structure

source

The DL_POLY_2 Directory Structure

utility

The DL_POLY_2 Directory Structure

thermostat

Molecular Dynamics Algorithms | External Fields | Integration of the Rigid | Integration of the Rigid | The DL_POLY_2 Multiple Timestep | The CONTROL File Directives | Message 430: error - | Message 464: error -

Berendsen

Berendsen Barostat | Berendsen Barostat | Integration of the Rigid | Linked Rigid Bodies | Test Case 4: Shell | Test Case 5: Shell

Nosé-Hoover

The Hoover Barostat | The Hoover Barostat | Integration of the Rigid | Linked Rigid Bodies | Constructing Nonstandard Versions | Test Case 3: An

units

DL_POLY

Units | Summary of Statistical Data

energy

.

pressure

Units | Units | The Hoover Barostat | The CONTROL File Directives | Pressure units: | Summary of Statistical Data

Verlet neighbour list

Ewald Sum | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | The DL_POLY_2 Multiple Timestep | Distributing the Nonbonded Terms | Distributing the Nonbonded Terms | Distributing the Nonbonded Terms | Three Body Forces | Metal Potentials | Constructing Nonstandard Versions | Constructing Nonstandard Versions | Further Comments on the | Further Comments on the | Message 106: error - | Message 107: error - | Message 108: error - | Message 109: error - | Message 110: error -

WWW

The DL_POLY Package | Obtaining the Source Code | Obtaining the Source Code

X-PLOR

The DL_POLY Package