Forcefield-Based Simulations


Index

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




Index

A

ab initio, 11
ABM4 integrator, 180
compared with Verlet velocity integrator, 188
absolute free energy
algorithm, 241
calculation, 239
conformational searching, 249
constraining dynamics, 250
convergence, 252
dynamics running averages, 254
errors, 251, 252
example, 246
ideal solid, 241
intervals, number, 251
reference state, 245, 246
setting up, 248
spring constants, 250, 253
Adams-Bashforth-Moulton integrator, 180
adiabatic compliance tensor, 193
adiabatic compressibility, 193
adiabatic ensembles, 189
Alagona, G., 262
Allen, M. P., 107, 193, 205, 210, 255
Allinger, N. L., 60, 258, 261
AMBER, 60
atom types, 45
atom types for carbohydrates, 46
characteristics, 21
distance-dependent dielectric, 116
functional form, 45
hydrogen-bond term, 45
1-4 nonbond interactions, 113
amino acids, 23, 48, 51
Andersen, H. C., 192, 210, 220, 255
angles
constraints, 100, 219, 220
atom types
assigning, 70
asterisks, 75
equivalences, 75
forcefield parameter assignment, 74
wildcarding, 75, 77
wildcarding, precedence, 77
X, 75
atomic positions, poorly defined, 92
atomic velocities, 195
atoms
fixing, 92
forces on, 166
types, 69, 263
typing, 68
atom-type charge, 71
Austin, N., 57, 262
automatic atom types, 30, 51

B

Bash, P. A., 260
Becker, J. M., 257
Berendsen equation, 200
Berendsen, H. J. C., 200, 207, 209, 255, 260, 261
Beveridge, D. L., 165, 259
BKS forcefield, 55
bold type, meaning, 7
bond increments, 30, 51
bonds
between symmetrically related objects, 110
constraints, 100, 219, 220
Born-Oppenheimer equation, 11
Born, M., 11, 255
Boyd, D. B., 256
Brady, J. W., 257
Brooks, B. R., 22, 47, 255
Brooks, C. L., 237
Brooks, C. L., III, 117, 217, 255
Brown, D., 210, 255
Brown, F. K., 260
Bruccoleri, R. E., 255
Brunger, A. T., 255
buffer region, 123
building models, 66
bulk modulus, 194
Burchart forcefield, 55
implementation, 56
Burchart-Dreiding forcefield, 56
Burchart-Universal forcefield, 56
Burchart, E. de Vos, 55, 255

C

calculation
dynamics, 221
calculations
controlling, 15, 91, 213
loops, 213
minimization, 157
carboxylates, 125
Carruthers, L. M., 259
Cartesian and crystal axes, 104, 105
Cartesian coordinates, 18, 104
Casewit, C. J., 21, 40, 255, 256, 260
Case, D. A., 262
Catlow, C. R. A., 136, 256
cell multipole method, 128
accuracy, 131
and nonbond interactions, 131
and system size, 131
CPU time, 131
derivation of, 128
Cerius2·Morphology module forcefields, 51
CFF forcefields
availability, 25
functional form, 27
CFF91
atom types, 271, 294
automatic parameter assignment, 77
characteristics, 20
functional form, 28, 30
out-of-plane coordinate, 28
"CFF93", 59
CFF95
additional information, 30
limitations, 30
charge groups
cutoffs and, 124
defined, 124
charges
assigning, 73
CHARMm
characteristics, 21, 46
functional form, 46
Cheetham, A. K., 259, 262
chemical perturbations, 233
chirality, 45
Ciccotti, G., 260
Clark, J. H. R., 210, 255
classic harmonic oscillator, 13
classical forcefields
availability, 43
types, 43
Colwell, K. S., 255, 256, 260
common structures, finding, 216
compressibility, 194
computation
costs, 92, 152
efficiency, 118
time, 108
conformation
searches, 215
conformational changes
forcing, 93
conformational energies, 167
conformational energy barriers, 214
conformational searches, 175, 215
conformations
comparing, 94
searches, 175, 191
stable, 140
consensus dynamics, 215
Consistent Valence Forcefield, see CVFF and forcefields
constraints, 99
creating, 99
definition, 15, 89
dynamics, 217
Coulombic
interactions, 28, 112
terms, 18, 50
cross terms, 16, 28, 50, 162
definition, 18
importance of, 50
Cross, P. C., 262
crystals
environment, 103, 137
phase transitions, 209
surface contributions, 137
cutoff distance
effect on van der Waals energy, 119, 120
switching function, 121
cutoffs
double, 126
methods, 117
periodic systems, 107, 108
variable names in versions 2.9.5 and 95.0, 122
CVFF
atom types, 51
automatic parameter assignment, 77
characteristics, 22
functional form, 49

D

Dauber-Osguthorpe, P., 48, 256
Dauber, P., 257, 258
Decius, J. C., 262
Deem, M. W., 137, 256
Demontis, P., 57, 256
Denouden, C. J. J., 259
density, periodic boundary conditions, 205
diagonal terms, 49
dielectric constant, 51, 116
Dielectric parameter, 117
diffusion coefficients, 175
Ding, H. Q., 128, 131, 256
DiNola, A., 255
Dinur, U., 20, 256, 258, 259
dipole-dipole interactions, 112
disordered periodic systems, 127
distance constraints, 100
distance restraints, 96
potential form, 96, 97, 98
distorted structures, 162
Dist_Dependent parameter, 117
DNA, 22
Dreiding forcefield
atom type naming, 42
availability, 34
characteristics, 21
versions, 43
dynamics, 173
ABM4, 180
achieving equilibrium, 200
algorithms, 177
Andersen method, 203, 210
animation, 221
appropriate ensemble, 194
artifacts, 184
Berendsen method, 200, 209
blowing up, 184
canonical ensemble, 191
colliding hydrogen atoms example, 183
computing time, 217
consensus, 215
constant-energy, constant-volume ensemble, 190
constant-pressure, constant-enthalpy ensemble, 192
constant-temperature, constant-pressure ensemble, 191
constant-temperature, constant-stress ensemble, 191
constant-temperature, constant-volume ensemble, 191
constraints, 220
constraints and restraints, 217
continuing a run, 229
data-collecting stage, 222
definition, 12
direct velocity scaling, 199
double cutoffs and, 126
energy conservation example, 187
equilibration, 200, 222
files, 229
generating statistical ensembles, 175
Hoover, 201
impulse, 216
initial velocities, 196
integration errors, 183, 187
integrators, 177
Langevin, 216
lengths of run stages, 222, 223
limitations, 183
liquid simulations, 210
microcanonical ensemble, 190
multiple timesteps, 126
Nosé, 200
Nosé-Hoover, 201
Nosé-Hoover method and fictitious mass, 201, 202
Nosé-Hoover method and integrator, 203
Nosé-Hoover method and relaxation time, 202
Nosé-Hoover method and timestep, 202
Nosé-Hoover thermostat, 201
obtaining accurate fluctuations, 193
Parrinello-Rahman method, 211
periodic systems, 207
preparing the system, 223
pressure, 203, 209

E

Eichinger, B. E., 260
Einstein solid, 243
elastic constant, 194
electronic motion equation, 11
electrostatic interactions, 45, 50
energy
barriers, 216
contributions of terms, 15
enthalpy, 193
at absolute zero, 164
binding, 165
entropy, 165, 168, 252
equilibrium thermodynamic properties, 193
Ermer, O., 4, 152, 256
ESFF
angle rules, 37
angle types, 36
atom types, 289
availability, 33
bond energy, 35
bond rules, 35
characteristics, 21
charges, 37
electronegativity, 38
energy expressions, 35
functional form, 35
hardness, 38
ionization potential, 39
out-of-plane term, 37
periodic table coverage, 40
torsion rules, 37
torsion term, 37
van der Waals interactions, 39
ethane, 237
Ewald calculations
accuracy, 137
and nonbond interactions, 138
and system size, 137
computational load, 136
CPU time, 137
dipole moment, 134
2D periodicity, 138
Ewald, P. P., 132, 256
Ewig, C. S., 20, 30, 257, 258
explicit image model, 107, 108

F

fentanyl, 246
phi,psi map, 247, 249
Field, M., 257
files
.car, 239, 248
.cli, 248, 253
.cor, 248
dynamics, 229
forcefield, 75
.frc, 30, 51
.his, 252
history, 252
.inp, 239
.mdf, 70, 239
molecular data, 70
.out, 251, 254
output, 251
.tot, 239, 252, 253
Fisher, J., 260
Flannery, B. P., 260
Fleischman, S. H., 237
Fletcher, R., 150, 163, 256
fluids, nonviscous, 204
fluorescence depolarization rates, 221
forcefields
aluminophosphates, 55
AMBER, 44
and modeling programs, 1
atom type equivalences, 75
atom types, 69
automatic, 76
automatic parameter assignment, 76
broadly applicable, 21, 33
Cerius2·Morphology module, 57
choosing, 18
classical, 21
components, 12
crystal morphology, 57
CVFF, 48
definition, 4, 12
editing, 80
ESFF, 35
functional forms, 12, 16
general sequence of activities for using, 66
glass, 52
graphical and standalone-mode use, 65
graphical molecular modeling interfaces, 65
Homans AMBER, 21
importance, 4
internal coordinates, 18
limitations, 15
mechanical approach, limitations of, 15
mechanical vs. quantum mechanical approach, 13
MSXX, 54
old, 58, 59
parameters and atom types, 74
purpose, 13
quantum calculations and, 26
quantum mechanical parameterization, 26
reading parameters, 66
rule-based, 21, 33
second-generation, 20, 25
selecting, 68
silicas, 55
sorption, 57
sorption onto zeolite structures, 57
special-purpose, 22
standalone, 65
summary table, 23
terms, 12
types, 19
types of molecules, 22
unsupported, 58, 59
using, 65
zeolites, 55
frictional coefficients, 216, 221

G

Garofalini, S. H., 52, 256, 258, 260, 262
Gaussian-Legendre quadrature method, 236
Gelin, B. R., 259
general multipole moments, 130
generating Cartesian coordinates, 67
Genest, M., 256
Ghio, C., 262
ghost
images, 108
list regeneration, 108
molecules, 107, 109
Giammona, A., 257
glass forcefield, 51, 52
automated setup, 54
functional form, 52
global minimum, 164, 214
glycoproteins, 45
Goddard, W. A., 42, 54, 73, 115, 134, 136, 137, 256, 258, 259, 260
Greengard, L., 128, 131, 256
Gunsteren, W. F., 150, 256

H

Haak, J. R., 255
Hagler, A. T., 20, 26, 30, 51, 115, 119, 165, 256, 257, 258, 259, 261, 262
Halgren, T. A., 20, 32, 33, 115, 257
Hamiltonian, 241
Harris, F., 138
Harvey, S. C., 116, 257
Ha, S. N., 45, 46, 257
help, on-line, 6
hemoglobin, 131
Hessian matrix, 154, 161
computational cost, 152, 155
definition, 151
from second derivatives, 155
mathematical form, 154
preconditioning, 157
properties, 154
size, 152
heterogenous atom pairs, 114
Hill, J.-R., 20, 31, 257
Homans, S. W., 21, 44, 45, 257
Hoover, W. G., 201, 244, 257
Hwang, J. K., 165, 258
Hwang, M.-J., 20, 26, 30, 59, 258, 259
hydrocarbons, 51
hydrogen atoms, colliding, 184
hydrogen bonds, 51
hydrostatic pressure, 192, 204, 207, 211

I

Ikels, K. G., 259
image centering, 109
inexact line searches, 155
instantaneous kinetic temperature, 196
instantaneous pressure function, 205
interatomic distances, controlling, 96
internal energy, 194
International Tables for Crystallography, 104
IR line widths, 221
isothermal compressibility, 193, 223
isothermal ensembles, 189

J

Jacucci, G., 165, 260
Jorgensen, W. L., 237

K

Kao, J., 60, 258
Karasawa, N., 54, 115, 134, 136, 137, 256, 258
Karplus, M., 21, 46, 150, 255, 256, 258, 259
kinetic energy, 194
kinetic energy of nuclei, 168
King, G., 262
Kirkwood, J. G., 165, 258
Kitson, D. H., 119, 258
Klein, M. L., 256
Knaebel, K. S., 259
Kohler, A. E., 52, 258
Kollman, P. A., 260, 262
Kramer, G. J., 261

L

lattices, periodic, 103
Lee, M. A., 128, 131, 260
Lennard-Jones terms, 18, 50
Levitt, M., 147, 258
Levy, R. M., 216, 258
Lifson, S., 58, 147, 257, 258
Liljefors T., 60, 258
Lipkwowitz, K. B., 256
Li, S., 258
local minimum, 164

M

Maple, J. R., 20, 26, 28, 30, 258, 259, 261
Maxwell-Boltzmann
distribution, 195
equation, 195
factor, 239
Mayo, S. L., 21, 42, 60, 259
McCammon, J. A., 165, 216, 258, 259, 261
McGuire, R. F., 259
McQuarrie, 203, 259
methanol, 237
Mezei, M., 165, 233, 259
Mezei's algorithm, 233
Miller, G. W., 57, 259
minimization, 139
algorithms, 141, 161
constraints, 91
convergence, 162, 163
derivatives, 143, 163
efficiency, 141
energy expression, 141
energy zero, arbitrary, 164
initial relaxation, 148
iteration, defined, 146
line search, 143, 144
progressive, 92
restraints, 91
setting up, 158
significance, 164
strategies, 141, 157, 158
system size, 150, 152
uses, 2
minimizers
advantages, 155
Broyden-Fletcher-Goldfarb-Shanno, 154
comparative efficiency, 157
conjugate gradients, 149, 162
Davidon-Fletcher-Powell, 154
differences among Newton methods, 154
discontinuities in potential energy surface, sensitivities to, 126
limitations, 152
Newton-Raphson, 151, 152, 161
Newton-Raphson, algorithm, 153
quasi-Newton-Raphson, 154
steepest descents, 146, 147, 148
truncated Newton-Raphson, 155
minimum image model, 107, 207
MMFF
availability, 26
energy expression, 32
modeling incomplete systems, 91
molecular dynamics, see dynamics
molecular mechanics, 12
molecular modeling program, difinition, 5
Momany, F. A., 22, 46, 58, 259
monomer definitions, 66
Montgomery, 255
Morphology/Lifson forcefield, 58
Morphology/Momany forcefield, 58
Morphology/Scheraga forcefields, 58
Morphology/Williams forcefield, 58
Morse potential, 49, 162
harmonic potential, compared with, 50
MSI's website, 6, 116
MSXX, 54
Morse functional form, 55
parameterization, 54
Mumby, S. J., 261
Murcko, M. A., 46, 262

N

Nachbar, R. B., 20, 33, 257
Naider, F., 257
natural response functions, 193
neighbor list, 123
Némethy, G., 58, 259
Newsam, J. M., 256
Newton's equation of motion, 11, 176
Nguyen, D. T., 262
NMR relaxation times, 221
nonbond interactions, 50
cell multipole method, 128
cutoff distance and, 118, 119
definition, 18
Ewald calculations, 132
system size and, 117
nonbond list, 123
nonbond terms, 16
nonpolar hydrogens, 45
Norgett, M. J., 136, 256
normal mode analysis, 163
Nosé, S., 200, 202, 259
Nowak, A. K., 259, 262
nuclear motion equation, 11
nucleic acids, 44
number density, 221

O

off-diagonal terms, see cross terms
Olafson, B. D., 255, 259
oligosaccharides, 45
Oppenheimer, J. R., 11, 255
Osguthorpe, D. J., 256

P

Parrinello, M., 192, 211, 259
partition function, 241
peptides, 22
periodic boundary conditions, 207
definition, 103
periodic systems
disordered, 127
dynamics, 191, 193, 205, 207
Ewald calculations, 132
Peterson, B. K., 259
Pettitt, B., 255
Pickett, S. D., 57, 259
polymer forcefield, 52
polymers, 44
polysaccharides, 44, 45
polyvinylidene fluoride forcefield, 51, 54
Postma, J. P. M., 255, 261
Post, M. F. M., 259
potential energy surface, 10, 11, 16
discontinuities, 126
empirical fit, 11, 12
non-quadratic, 161
saddle points, 170
shape of, 167
transition states, 170
water molecule, 17
Potentials Forcefield, 71, 73
Pottle, M. S., 259
Powell, M. J. D., 150, 260
pressure, 194
and correct statistical ensemble, 208
calculation, 205
changing, 209
control, 208
functional form, 203
periodic boundary conditions, 205
sign conventions, 205
thermodynamic, 205
units, 204
virial theorem, 205
Press, W. H., 163, 181, 236, 260
Profeta, S. Jr., 262
proteins, 22, 44
protonated amines, 125
p1_4 parameter, 114

Q

quantum effects, 164
quantum mechanical probability function, 14
quartz, 132
Quirke, N., 165, 260

R

radius of gyration, 221
Rahman, A., 211, 259
Rappé, A. K., 21, 40, 41, 42, 73, 255, 256, 260
rattle command, 99
Ravimohan, C., 237
Ray, J. R., 191, 193, 260
reading models, 66
Reeves, C. M., 150, 256
Ree, F. H., 244
Reidl, D., 104, 260
relative free energy
benchmark calculation, 237
convergence, 236, 239
degrees of freedom, 238
drift, 239
example, 237
FDTI, 233, 235, 236
finite difference thermodynamic integration, see FDTI
functional form, 236
perturbation method, 234
results, 239
setting up, 238
thermodynamic cycle, 237
residue definitions, 66
restraints, 16, 140
angle, 100
definition, 15, 89
distance, 96
dynamics, 217
inversion, 102
torsion, 101
Rigby, D., 32, 260, 261
RNA, 22
Roberts, V. A., 256
Rokhlin, V. I., 128, 131, 256
Rone, R., 22, 46, 259
Rosenthal, A. B., 52, 260
rotational barriers, heights, 167
Runge-Kutta integrator, 181
Ryckaert, J.-P., 219, 260

S

saddle points, 163
Sauer, J., 20, 31, 257
Scale_Terms Parameters, 114
Scheraga, H. A., 259
Schmidt, K. E., 128, 131, 260
Schrödinger equation, 10
Set Parameters, 117
setting up calculations, 67
Sharon, R., 257
shear stress, 204
shielded dielectric function, 116
Shi, S., 260
simulated annealing, 215
simulation engine, definition, 4
Singh, U. C., 165, 237, 260, 262
Sinha, S. K., 256
Skiff, W. M., 260
small molecules, 44
Smit, B., 259
solvent, 103, 106
Sorption Demontis forcefield, 57
Sorption Pickett forcefield, 57
Sorption Yashonath forcefield, 57
Soules, T. F., 52, 261
special-purpose forcefields
availability, 51
characteristics, 52
specific heat, 193, 194, 223
specific heat at constant pressure, 193
spectral densities, 221
spline switching nonbond cutoff, 121
Sprague, J. T., 60, 261
Stapleton M. R., 262
States, D. J., 255
statistical ensembles, 175, 188
Stern, P. S., 257
Stockfisch, T. P., 258, 259
Straatsma, T. P., 165, 261
stress, 204, 211
control, 208
sign conventions, 205
tensor components, 192
units, 204
stress-strain relationship, 192, 204, 211
structural similarities, 216
Sun, H., 20, 31, 32, 260, 261
surface charges, 137
Sussman, F., 262
Swaminathan, S., 255
Swift, J. F. P., 259
switching atom defined, 124
switching function, effect on nonbond energy, 122
symmetry relations, 109

T

Tai, J. C., 258, 261
Tembe, B. L., 165, 261
temperature, 194
and average kinetic energy, 196
and correct statistical ensemble, 197
calculation of, 196
control, 203
damping, 200
distribution of atomic velocities, 195
integration errors, 187
nonperiodic system, 196
nonzero, 173
periodic system, 197
template atoms, 94
template forcing, 93, 141
functional forms, 93
tensile stress, 204
Tesar, A. A., 52, 261
tethering, 92, 95
functional forms, 95
Teukolsky, S. A., 260
Thacher, T. S., 259
thermal expansion, 193, 194
thermodynamic cycle, 165
thermodynamic ensembles, 175
thermodynamic response function, 191
thermodynamic temperature, 196
Thomas, J. M., 259, 262
Tildesley, D. J., 107, 193, 205, 210, 255
timestep length in dynamics, 181
Tolleanaere, J. P., 246
torsions
forcing, 101
restraints, 101, 102
trajectory
animation, 221
contents, 220
definition, 176
length, 223
uses, 221
transition states, 167

U

united-atom representation, 45
Universal forcefield
atom type naming, 41
availability, 34
characteristics, 21
charges, 42
implementation, 40
parameter generation, 41
versions, 42

V

valence exclusions, 113
valence interactions, 16
van Beest, B. W. H., 55, 261
van der Waals
combination rules, 114
cutoff distance and, 119, 120
Ewald calculations, 132
interaction potential, 183
interactions, 28, 45, 50
van Gunsteren, W. F., 255
van Santen, R. A., 261
Varshneya, A. K., 52, 261
Verlet leapfrog integrator, 178, 179
Verlet velocity integrator, 178, 179
compared with ABM4 integrator, 188
Verlet, L., 179, 261
Vetterling, W. T., 260
vibrational calculations, 169
computational costs, 172
cross terms and, 172
entropy, 171
forcefield accuracy and, 172
free energy, 167
frequencies, 50, 152, 167, 170
from potential energy surface, 168
harmonic, 139
imaginary frequencies, 170
normal mode analysis, 152
prerequisites, 170
quality, 170
quantum mechanical equation, 171
uses, 167
virial, 194
viscous fluids, 217
volume, periodic boundary conditions, 205

W

Waldman, M., 20, 115, 258, 262
Warshel, A., 165, 258, 262
Watanabe-Austin forcefield, 57
Watanabe, K., 57, 262
water, 48
constrained, 220
fixed-geometry model, 100, 220
SPC, 100, 220
TIP3P, 100, 220
Weiner, P., 262
Weiner, S. J., 21, 44, 60, 262, 270
Wiberg, K. B., 46, 262
Williams, D. E., 58, 262
Wilson, E. B., 28, 168, 262
Wolff, J., 256
Wolynes, P. G., 259
Woodcock, L. V., 52, 262

Y

Yang, Y., 260
Yan, L., 260
Yashonath, S., 57, 256, 262
Yuh, Y., 261

Z

zeolite forcefield, 51, 52
zero-point corrections, 164, 167, 171
Zirl, D. M., 52, 256, 262


Last updated October 02, 1997 at 12:04PM PDT.
Copyright © 1997, Molecular Simulations, Inc. All rights reserved.