Cerius²·Forcefield Engines


Index

A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z



A

accuracy 24
adiabatic compressibility 89
analysis 65
ANALYSIS card 66
Analysis Input control panel 68, 69, 70, 71
Analysis module 66
Analysis Output control panel 71, 72
Analysis Show Frames control panel 70, 71
Analysis Statistics control panel 71, 72, 73, 74, 75, 88
Anneal Dynamics Preferences control panel 53
Atom Constraints control panel 21
atom types
additional information 99
and energy terms 106
attributes 14, 15, 99
automatic assignment 10, 13, 99
calculated 15
creating 99, 100
defining 99
deleting 100
editing attributes 99, 100
generic 106
in forcefields 98
labels 10, 13, 16
manual assignment 13, 15
number of lone-pair electrions 100
palette 100
reassigning 13, 14
selected atoms 15
selecting 100
undefined 14
verifying assignments 13
wildcard 106
X 106, 108
atom typing rules
creating 99, 104
criteria 101, 104, 105
deleting 105
display 102
editing 99, 104
examining 103
example 101
illustration 101
implementation 102
navigating the tree structure 103
studying 98, 103
tree structure 101
what they do 100
atoms
allowing to move 21
constraining 19
dipole calculations 87
fixing 19, 21
mean-square displacement 76
radial distribution 83
restraining 19
velocity autocorrelation 79
atom-type charge 14
editing 100
parameterized 14
atom-type element 100
atom-type hybridization 15
editing 100
atom-type mass 14
editing 100
implicit hydrogens 15
Attribute Assignments control panel 15, 16
autocorrelation function 78
autocorrelation studies 49
Automate Energy Setup control panel 9, 10

B

Berendsen, H. J. C. 49, 93
Blends module 31
Block Average Preferences control panel 75, 91
bold type, meaning 4
Bond Order control panel 16, 17
bond orders 10
bond types 10

C

C2·Analysis module 65, 66
C2·Charges module 18
C2·Dynamics module 45
C2·FFE module 96
C2·Minimizer module 34
C2·MMFF module 7, 35
C2·OFF module 7
C2·Tables module 72
Casewit, C. J. 93
cell constraints 21
Cerius2 Interrupt window 61
CFF 12
editing 95, 107
CFF forcefield 12
charge equilibration method 17, 18
charges
assigning 14, 17
calculation 18
dipole calculations 86
editing 17
labeling 19
net 17
updating 53
CHARGES card 18
Charges control panel 18, 19
Charges module 17, 18
Color Selected Objects control panel 21
Colwell, K. S. 93
compressibility 81, 84
computational expense 19, 23, 24
constraints 19
and other modules 20
setting 21
technical note 20
verifying assignments 21
Coulomb Ewald Preferences panel 26
Coulomb Preferences control panel 25, 26, 27
Coulombic interactions 24, 25
Ewald settings 26
method 25
settings 25
current energy 42
CVFF
editing 95, 107

D

Default Parameters control panel 32
dielectric constant 89
diffusion constant 78
DiNola, A. 93
dipole autocorrelation 87
Dipole control panel 87, 88
dipole moment 86, 87, 89
dipole vector 86, 87
dipole-dipole correlation function 86, 87, 88
dipole-dipole power spectrum 86, 87, 88
directories 97
displacement analysis functions 75
Distribution Preferences control panel 74, 75
Dreiding forcefield
charges 14
default preferences 118
dynamic properties 78, 80
dynamics 43
additional information 44
appending to a previous run 63, 64
atomic velocities 48, 49, 57, 61, 63, 64
calculation conditions 46
charge recalculation 53
collecting data 60
constant conditions 47
constant-pressure/constant enthalpy 47
constant-pressure/constant-temperature 47
constant-volume/constant-energy 47
constant-volume/constant-temperature 47
continuing 62
continuing saved runs 62
continuous runs 58
coordinate data 63, 64
cumulative property averaging 50, 55, 56
data-collection stage 60
energy 47
enthalpy 47
equilibration stage 59
explicit initial velocity vectors 49
external hydrostatic pressure 51
extracting input from a previous run 63, 64
frames 64
graphs 54, 55, 61, 71
heat bath 48, 50
impulse dynamics 48, 49
information output 54, 56
initial temperature 48, 49, 53
input 61, 62, 63
interrupted runs 61, 62
kinetic temperature 47
mass-like parameter W 51
model display 54, 56
NPH 47, 48, 49, 51
NPT 47, 48, 50, 51
NVE 47, 48, 49
NVT 47, 48, 50
original structure 56
output 54
output frequency 56, 57
part of a model 19
periodic systems 50
plots 54
preparing the system 59
prerequisites 44
pressure 47, 50, 51
pressure "bath" 51
production run 60
quenched 52, 53, 55, 58
Reset controls 61
restarting 61, 62, 63
resuming 61
run length 54
simulated annealing 52, 53, 55, 58
starting the run 57
statistical ensembles 48
step counter 61
stress 51
stress "bath" 51
tables 72
target temperature 48, 49
temperature 47, 50, 53
temperature control method 50
temperature cycles 52, 53
temperature scaling 48, 50
temperature window 48, 50
thermodynamic temperature 48
thermodynamics ensembles 46
timestep 54
trajectory 53, 54, 57, 62, 63
velocity scaling 48
volume 47
with minimization 52, 53
Dynamics module 45
Dynamics Output Preferences control panel 55, 56, 57
DYNAMICS SIMULATION card 45
Dynamics Simulation control panel 47, 49, 50, 51, 52, 53, 54, 57, 58, 59, 60, 61, 62, 63, 64
Dynamics Trajectory Input control panel 57, 60, 61, 63, 64
Dynamics Trajectory Output control panel 55, 57, 59

E

Einstein relation 77
electrostatic interactions 24
electrostatic properties 89
energy expression
automatic setup 10, 30
checking validity 32
choosing terms 29
constraints 20
excluding default terms 29
including nondefault terms 29
manual setup 30, 31
preparing 9
printout 31
reinitializing 10
repeating setup 31
respecifying setup 30
setup 30
terms 105
undefined terms 14, 29
when setup is needed 31
Energy Expression control panel 31, 32
Energy Minimization control panel 36, 38, 39, 41, 42
energy of current structure 42
energy terms 105
additional information 105
and atom types 106, 107
atom types, searching 108
defining 107
deleting 108
editing 107
examining 107
functional form 105, 107, 108
how applied to atom types 106
ignoring 108
in forcefields 106
parameters 105, 107, 108
removing 108
searching atom types 108
setting to zero 108
specific atom types 108
studying 105, 107
undefined 106, 108
wildcards 108
Energy Terms Selection control panel 23, 29, 30
enthalpy 89
constant 89
Ewald sum method 25
2D periodic systems 27
geometric combination rule 25
off-diagonal parameters 25
problems with second derivatives 27
settings 26
Ewald, P. P. 25, 93

F

FFE module 96
file browsers 9, 63, 97
files
.arc 68
.atrj 55, 57, 63, 68
converter for forcefield parameters 120
documentation at website 111
forcefield parameters 111
.his 68
minimization output 41
.qtrj 55, 57, 63, 68
tables 72
trajectory 52, 54, 57, 63, 68
trajectory, analysis 65
.trj 55, 57, 63, 68
Fluctuations control panel 90, 91
Force Field Atom Type Attributes control panel 99, 100
Force Field Atom Type Palette control panel 15, 16, 100, 102, 104, 110
Force Field Atom Typing control panel 15, 16
Force Field Atom Typing Rules control panel 102, 104, 105
FORCE FIELD EDITOR card 96
Force Field Editor module 95, 96
Force Field Load Preferences control panel 11, 98
forcefields
additional information 9, 97
alternative terms 29
and parameter quality 32
automated loading 9, 10
automated setup 9, 11
CFF 12
choice 8
creating 95, 99
customizing 95
default energy terms 28
editing 95, 106
energy expression 31
energy terms 106
energy terms available 29
energy terms, editing 105
filenames 8
loading 11, 97, 98
manual loading 11
optional terms 29
parameters, editing 105
recommendations 8
reinitializing settings 10
saving 98
specifying 10
studying 95
verification 95
fractional bond orders
automatic assignment 10, 16
labels 10, 17
manual assignment 16
reassigning 16
UFF 16
verifying assignments 17
when to assign 16

G

Gasteiger method 17, 18
Gasteiger, J. 18, 93
Goddard, W. A. 18, 25, 93
GRAFDREIDING1.00 forcefield
technical note 15
graphs
dipole moment 88
dipole vector 88
dipole-dipole correlation function 88
dipole-dipole power spectrum 88
MSD 76, 77
power spectrum 81
properties 73, 90
RDF 83
results 73
simulations 73
structure factor 86
VACF 79
Gruneisen parameter 89

H

Haak, J. R. 93
Halgren, T. A. 7, 93
harmonic restraints 19
help, on-screen 3
Hoover, W. G. 48, 93
hybridization 15
Hydrogen Bond Preferences control panel 26
hydrogen-bond interactions 25, 28

I

Impulse Dynamics Preferences control panel 49
infrared spectra 78, 80, 86
interaction energy terms 105
interatomic vector lengths 81
internal energy 89
Inversion Preferences control panel 29, 30
inversion terms 29
inversions about a common central atom 30
isobaric heat capacity 89
isoenthalpic Joule-Thomson coefficient 89
isometric heat capacity 89
isothermal compressibility 89
isothermal Joule-Thomson coefficient 89
italic type, meaning 4

K

Karasawa, N. 25, 93
Kirkwood-Frohlich equation 89

L

Load Force Field control panel 11, 97, 98
Load Preferences control panel 10

M

Marsili, M. 18, 93
Mean Squared Displacement control panel 76, 77, 78
mean-square displacement 75
linear fit 78
Measurements control panel 74
Mechanical Properties module 51
mechanical properties of bulk materials 37
minimization
additional information 34
algorithms 36
convergence criteria 38
graphs 39, 40, 71
information output 39
maximum displacement 36
model display 40
number of iterations 39
original structure 40
output 40
output frequency 40, 41
part of a model 19
periodic systems 37
plots 39
prerequisites 34
pressure 37
search precision 36
smart minimizer 36
starting the run 41
stress 37
tables 72
termination criteria 38
trajectory 41
with dynamics 52, 53
MINIMIZER card 34
Minimizer Cell Constraints control panel 21
Minimizer Convergence Criteria control panel 38
Minimizer External Stress control panel 37
Minimizer module 34
Minimizer Output control panel 40
Minimizer Preferences control panel 36
MMFF
automatic loading 8
MMFF card 7, 35
MMFF card deck 7, 35
MMFF Energy Minimization control panel 12, 26, 36, 38, 39, 40, 41, 42
MMFF Minimizer Controls control panel 36, 38, 39
MMFF module 7, 35
MMFF Nonbonded Preferences control panel 26, 28
MMFF Output Commands control panel 40
models
animation 70
anisotropic 76
bad initial geometry 11
biasing the structure 21
collection of, as trajectory 67
conformation from graph 70
conformations 70
current energy 42
display during minimization 40
dynamics 46
energy expression 30, 108
information 71
large 25
minimization 35
nonperiodic 25, 82, 84
partially known structure 19
partially rigid 19
periodic 25, 50, 77, 82, 85, 90
significant changes 31
small 24
strained 11
molecular dynamics 43
Molecular Dynamics Controls control panel 49, 50, 53, 56, 60, 61, 62
Molecular Simulations, Inc.
customer support 3
website 3, 111
Morphology module 31
Morse functional form 11
MSXX forcefield
technical note 11

N

Nachbar, R. B. 7, 93
neighbor list 27
neighbor search algorithms 27
nonbond interactions 24
2D-periodic models 25
choosing the method 26
cutoff distance 24, 26
direct method 24
Ewald sum method 25, 26
nonbond list 25
settings 26
spline method 24
spline-off distance 25, 26
spline-on distance 24, 26
Nosé, S. 48, 93
NPH Dynamics Preferences control panel 50, 51, 52
NPT Dynamics Preferences control panel 50, 51, 52
NVE Dynamics Preferences control panel 50
NVT Dynamics Preferences control panel 50

O

OFF METHODS card deck 34, 45, 66
OFF module 7
OFF SETUP card deck 7, 18, 96
OPEN FORCE FIELD card 7
Open Force Field module 7
relation to other modules 7
optimization policy 27
ordering 81, 84
out-of-plane terms 29
out-of-planes about a single central atom 30

P

packing 81, 84
parameter quality 32
Parameter Quality control panel 32
pf program 120
phase transitions 81, 84
point charges 17
Postma, J. P. M. 93
power spectrum 79, 80
frequency resolution 80
resolution 80
prerequisites 2
pressure 89
constant 89
properties, fluctuation 89

Q

Quench Dynamics Preferences control panel 53

R

radial distribution function 81
computation time 82
cutoff distance 82
Fourier transform 84
groups 81, 83
Raman spectra 78, 80
Rappé, A. K. 18, 31, 93, 109
RDF control panel 83, 86
restraints 19
enabling 23
force constant 21
functional form 20
removing 23
selecting atoms 21
setting 23
verifying assignment 23
Restraints control panel 21, 23
results, analysis 65
block average 74, 90
dipole functions 86
fluctuations 89
frequency distribution 74
graphs 71
highest values 75
histogram 74
history 74
loading trajectory 67
lowest values 75
mean-square displacement 75
measurements 74
model display 70
MSD 75
properties 74, 90
RDF 81
running average 74, 90
saving to table file 72
selecting 73
single conformation 71
subset of results 68
text window 71
time-dependent profile 74
VACF 78
velocity autocorrelation 78
rigid bodies 22

S

Save Force Field control panel 98
Save Model control panel 71
self-diffusion constant 75, 77
simulated annealing 52
Skiff, W. M. 93
Sorption module 31
sound, speed 89
stress-strain curve 37, 51
structure factor 84
cutoff distance 85
k-space interval 85
resolution 85

T

tables 72
temperature 89
constant 89
thermal effects 78, 80
thermal pressure coefficient 89
thermodynamic properties 89
Torsion Preferences control panel 29, 30
torsion terms 29
torsions about a common bond 29
torsions exocyclic to aromatic rings 29
trajectory
analysis 65
collection of models as 67
frame information 71
frames 68
graphs 71
loading 67
model display 70
partial 68
saving to table file 72
searching 75
single frame, saving model 71
single frames 70
stepping through frames 70
typewriter font 4
typographical conventions 4

U

UFF
bond types 16
bond typing 16
charges 17, 53
default preferences 118
defined parameters 109
editing generator parameters 105, 110
examining generator parameters 110
generator parameters 109
hybridization 15
parameter generation 31, 109
single-atom-type parameters 105, 109
Universal Force Field Generator control panel 109, 110
unnormalized distribution function 82

V

van der Waals interactions 24
attractive 25, 26
geometric combination rule 25
method 25
nonidentical atom types 25
repulsive 25
settings 25
Van Der Waals Preferences control panel 25, 26, 28
van Gunsteren, W. F. 93
VDW Ewald Preferences control panel 26, 27
Velocity Autocorrelation control panel 79, 80, 81
velocity autocorrelation function 78
Fourier transform 79
velocity of sound 89
vibrational properties 78, 80
Visualization Preferences control panel 23
volume 89
constant 89
volume expansivity 89

X

X-ray diffraction data 84


Index



Last updated July 09, 1998 at 07:49PM PDT.
Copyright © 1997, 1998 Molecular Simulations Inc. All rights reserved.