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, 192
compared with Verlet velocity integrator, 200
absolute free energy
algorithm, 255
calculation, 254
conformational searching, 263
constraining dynamics, 264
convergence, 267
dynamics running averages, 268
errors, 265, 267
example, 260
ideal solid, 255
intervals, number, 265
reference state, 259, 261
setting up, 263
spring constants, 264, 265, 268
Adams-Bashforth-Moulton integrator, 192
adiabatic compliance tensor, 206
adiabatic compressibility, 206
adiabatic ensembles, 201
Alagona, G., 276
Allen, M. P., 114, 206, 218, 223, 269
Allinger, N. L., 69, 272, 275
AMBER, 69
atom types, 54
atom types for carbohydrates, 54
characteristics, 22
distance-dependent dielectric, 124
functional form, 53
hydrogen-bond term, 53
1-4 nonbond interactions, 121
amino acids, 23, 56, 60
Andersen, H. C., 205, 223, 233, 269
angles
constraints, 107, 233
atom types
assigning, 77
asterisks, 83
equivalences, 83
forcefield parameter assignment, 82
wildcarding, 83, 85
wildcarding, precedence, 85
X, 83
atomic positions, poorly defined, 99
atomic velocities, 207
atoms
fixing, 100
forces on, 177
types, 77, 277
typing, 76
atom-type charge, 79
Austin, N., 66, 276
automatic atom types, 31, 60

B

Bash, P. A., 275
Becker, J. M., 271
Berendsen equation, 213
Berendsen, H. J. C., 213, 220, 222, 269, 274, 275
Beveridge, D. L., 176, 273
BKS forcefield, 64
bold type, meaning, 7
bond hybridization, 49
bond increments, 31, 60
bonds
between symmetrically related objects, 118
constraints, 107, 233
Born-Oppenheimer equation, 11
Born, M., 11, 269
Boyd, D. B., 270
Brady, J. W., 271
Brooks, B. R., 22, 55, 269
Brooks, C. L., 251
Brooks, C. L., III, 125, 230, 269
Brown, D., 223, 269
Brown, F. K., 275
Bruccoleri, R. E., 269
Brunger, A. T., 269
buffer region, 132
building models, 74
bulk modulus, 207
Burchart forcefield, 64
implementation, 64
Burchart-Dreiding forcefield, 65
Burchart-Universal forcefield, 65
Burchart, E. de Vos, 64, 269

C

calculation
dynamics, 234
calculations
controlling, 15, 98, 227
loops, 227
minimization, 169
carboxylates, 134
Carruthers, L. M., 273
Cartesian and crystal axes, 112, 113
Cartesian coordinates, 18, 112
Casewit, C. J., 21, 41, 269, 270, 274
Case, D. A., 276
Catlow, C. R. A., 145, 270
cell multipole method, 136
accuracy, 140
and nonbond interactions, 141
and system size, 140
CPU time, 140
derivation of, 137
Cerius2·Morphology module forcefields, 60
CFF forcefields
availability, 26
functional form, 28
CFF91
atom types, 285, 307
automatic parameter assignment, 85
characteristics, 20
functional form, 28, 31
out-of-plane coordinate, 28
"CFF93", 68
CFF95
additional information, 31
limitations, 31
charge groups
cutoffs and, 133
defined, 133
charges
assigning, 81
CHARMm
characteristics, 22, 55
functional form, 55
Cheetham, A. K., 273, 276
chemical perturbations, 247
chirality, 53
Ciccotti, G., 274
Clark, J. H. R., 223, 269
classic harmonic oscillator, 13
classical forcefields
availability, 52
types, 52
Colwell, K. S., 269, 270, 274
common structures, finding, 229
compressibility, 207
computation
costs, 100, 163
efficiency, 126
time, 116
conformation
searches, 228
conformational changes
forcing, 101
conformational energies, 178
conformational energy barriers, 227
conformational searches, 187, 228
conformations
comparing, 101
searches, 187, 204
stable, 150
consensus dynamics, 229
Consistent Valence Forcefield, see CVFF and forcefields
constraints, 107
creating, 107
definition, 15, 96
dynamics, 231
Coulombic
interactions, 28, 120
terms, 18, 59
cross terms, 16, 28, 59, 173
definition, 18
importance of, 59
Cross, P. C., 276
crystals
environment, 111, 146
phase transitions, 223
surface contributions, 146
cutoff distance
effect on van der Waals energy, 127, 128
switching function, 128
cutoffs
double, 134
methods, 125
periodic systems, 114, 115
variable names in versions 2.9.5 and 95.0, 130
CVFF
atom types, 60
automatic parameter assignment, 85
characteristics, 22
functional form, 57

D

Dauber-Osguthorpe, P., 56, 270
Dauber, P., 271, 272
Decius, J. C., 276
Deem, M. W., 146, 270
Demontis, P., 66, 270
Denouden, C. J. J., 273
density, periodic boundary conditions, 218
diagonal terms, 58
dielectric constant, 59, 124
Dielectric parameter, 125
diffusion coefficients, 187
Ding, H. Q., 137, 140, 270
DiNola, A., 269
Dinur, U., 20, 270, 272, 273
dipole-dipole interactions, 120
disordered periodic systems, 135
distance constraints, 107
distance restraints, 104
potential form, 104, 106
distorted structures, 173
Dist_Dependent parameter, 125
DNA, 23
Dreiding forcefield
atom type naming, 51
availability, 35
characteristics, 22
versions, 51
dynamics, 185
ABM4, 192
achieving equilibrium, 213
algorithms, 189
Andersen method, 216, 223
animation, 234
appropriate ensemble, 207
artifacts, 197
Berendsen method, 213, 222
blowing up, 198
canonical ensemble, 204
colliding hydrogen atoms example, 195
computing time, 231
consensus, 229
constant-energy, constant-volume ensemble, 203
constant-pressure, constant-enthalpy ensemble, 205
constant-temperature, constant-pressure ensemble, 204
constant-temperature, constant-stress ensemble, 204
constant-temperature, constant-volume ensemble, 204
constraints, 233
constraints and restraints, 231
continuing a run, 242
data-collecting stage, 235
definition, 12
direct velocity scaling, 212
double cutoffs and, 135
energy conservation example, 200
equilibration, 213, 235
files, 243
generating statistical ensembles, 187
Hoover, 213
impulse, 229
initial velocities, 208
integration errors, 195, 200
integrators, 189, 190
Langevin, 230
lengths of run stages, 236
limitations, 195
liquid simulations, 223
microcanonical ensemble, 203
multiple timesteps, 134
Nosé, 213
Nosé-Hoover, 213
Nosé-Hoover method and fictitious mass, 214, 215
Nosé-Hoover method and integrator, 216
Nosé-Hoover method and relaxation time, 215
Nosé-Hoover method and timestep, 215
Nosé-Hoover thermostat, 213
obtaining accurate fluctuations, 206
Parrinello-Rahman method, 224
periodic systems, 220
preparing the system, 236
pressure, 216, 222
pressure and cell size, 223
pressure control, 201, 204
pressure, effect of cutoffs, 223
quenched, 228
RATTLE algorithm, 233
reinitializing velocities, 243
relaxation time, 213
repeating a run, 189
reproducibility, 189
restarting a run, 242
results, 234
reviewing setup, 241
Runge-Kutta-4, 193
setting up, 235, 237
setting up SHAKE or RATTLE constraints, 231
SHAKE algorithm, 232
simulated annealing, 228
snapshots, 234
specifying output, 240
specifying run conditions, 238
specifying the integrator, 190
specifying the pressure- and stress-control methods, 222
specifying the temperature-control method, 211
specifying the thermodynamic ensemble, 202
specifying the timestep, 194
specifying types of simulations, 226
stability of numerical integration, 195
stages, 238, 242
starting a new run, 242
starting the run, 241
statistical ensembles, 201, 225
stochastic boundary, 230
stress control, 205
target temperature, 212
temperature control, 201, 204, 205, 210, 213
temperature cycles, 228
temperature effects, 199
theory, 188
timestep, 193
timestep length, 195, 232
trajectories, 234
trajectory, and absolute free energy calculation, 257
true canonical ensemble, 213
types, 225
unit cell changes, 204, 205
uses, 3, 185, 187
Verlet velocity integrator, 191
with minimization, 228

E

Eichinger, B. E., 274
Einstein solid, 258
elastic constant, 207
electronic motion equation, 11
electrostatic interactions, 53, 59
energy
barriers, 229
contributions of terms, 15
enthalpy, 205
at absolute zero, 176
binding, 176
entropy, 176, 179, 267
equilibrium thermodynamic properties, 206
Ermer, O., 4, 162, 270
ESFF
angle rules, 38
angle types, 37
atom types, 302
availability, 34
bond energy, 36
bond rules, 36
characteristics, 21
charges, 38
electronegativity, 39
energy expressions, 36
functional form, 36
hardness, 39
ionization potential, 40
out-of-plane term, 38
periodic table coverage, 41
torsion rules, 38
torsion term, 38
van der Waals interactions, 40
ethane, 251
Ewald calculations
accuracy, 147
and nonbond interactions, 147
and system size, 147
computational load, 145
CPU time, 147
dipole moment, 143
2D periodicity, 148
Ewald, P. P., 141, 270
Ewig, C. S., 20, 31, 271, 272
explicit image model, 115, 116

F

fentanyl, 260
phi,psi map, 261, 263
Field, M., 271
files
.car, 253, 264
.cli, 264, 268
.cor, 264
dynamics, 243
forcefield, 83
.frc, 31, 60
.his, 266
history, 266
.inp, 253
.mdf, 77, 253
molecular data, 77
.out, 266, 268
output, 266
.tot, 253, 266, 268
Fisher, J., 275
Flannery, B. P., 274
Fleischman, S. H., 251
Fletcher, R., 161, 174, 270
fluids, nonviscous, 217
fluorescence depolarization rates, 234
forcefields
aluminophosphates, 64
AMBER, 52
and modeling programs, 1
atom type equivalences, 83
atom types, 77
automatic, 84
automatic parameter assignment, 84
broadly applicable, 21, 34
Cerius2·Morphology module, 66
choosing, 19
classical, 22
components, 12
crystal morphology, 66
CVFF, 56
definition, 4, 12
editing, 88
ESFF, 36
functional forms, 12, 16
general sequence of activities for using, 73
glass, 61
graphical and standalone-mode use, 73
graphical molecular modeling interfaces, 73
Homans AMBER, 22
importance, 4
internal coordinates, 18
limitations, 15
mechanical approach, limitations of, 15
mechanical vs. quantum mechanical approach, 13
MSXX, 63
old, 67, 68
parameters and atom types, 82
purpose, 13
quantum calculations and, 27
quantum mechanical parameterization, 26
reading parameters, 74
rule-based, 21, 34
second-generation, 20, 26
selecting, 76
silicas, 64
sorption, 66
sorption onto zeolite structures, 66
special-purpose, 22
standalone, 73
summary table, 24
terms, 12
types, 20
types of molecules, 23
unsupported, 67, 68
using, 73
zeolites, 64
frictional coefficients, 230, 234

G

Garofalini, S. H., 61, 270, 272, 274, 276
Gaussian-Legendre quadrature method, 250
Gelin, B. R., 273
general multipole moments, 138
generating Cartesian coordinates, 75
Genest, M., 270
Ghio, C., 276
ghost
images, 116
list regeneration, 116
molecules, 115, 116
Giammona, A., 271
glass forcefield, 60, 61
automated setup, 62
functional form, 61
global minimum, 175, 227
glycoproteins, 54
Goddard, W. A., 43, 63, 81, 123, 144, 145, 147, 270, 272, 273, 274
Greengard, L., 136, 140, 270
Gunsteren, W. F., 161, 270

H

Haak, J. R., 269
Hagler, A. T., 20, 27, 31, 59, 123, 126, 176, 177, 270, 271, 272, 273, 275, 276
Halgren, T. A., 21, 33, 34, 123, 271
Hamiltonian, 255
Harris, F., 148
Harvey, S. C., 123, 271
Ha, S. N., 54, 271
help, on-line, 6
hemoglobin, 140
Hessian matrix, 165, 173
computational cost, 163, 165
definition, 162
from second derivatives, 168
mathematical form, 165
preconditioning, 168
properties, 165
size, 163
heterogenous atom pairs, 122
Hill, J.-R., 20, 32, 271
Homans, S. W., 22, 53, 54, 271
Hoover, W. G., 213, 258, 271
Hwang, J. K., 176, 272
Hwang, M.-J., 20, 27, 31, 68, 272, 273
hydrocarbons, 60
hydrogen atoms, colliding, 196
hydrogen bonds, 59
hydrostatic pressure, 204, 217, 220, 224
hypervalent molecules, 48

I

Ikels, K. G., 273
image centering, 117
inexact line searches, 165
instantaneous kinetic temperature, 209
instantaneous pressure function, 218
interatomic distances, controlling, 104
internal energy, 206
International Tables for Crystallography, 112
IR line widths, 234
isothermal compressibility, 206, 236
isothermal ensembles, 201

J

Jacucci, G., 176, 274
Jorgensen, W. L., 251

K

Kao, J., 69, 272
Karasawa, N., 63, 123, 144, 145, 147, 270, 272
Karplus, M., 22, 55, 161, 269, 270, 272, 273
kinetic energy, 206
kinetic energy of nuclei, 179
King, G., 276
Kirkwood, J. G., 176, 272
Kitson, D. H., 126, 272
Klein, M. L., 270
Knaebel, K. S., 273
Kohler, A. E., 61, 272
Kollman, P. A., 275, 276
Kramer, G. J., 275

L

lattices, periodic, 111
Lee, M. A., 137, 140, 274
Lennard-Jones terms, 18, 59
Levitt, M., 158, 272
Levy, R. M., 230, 272
Lifson, S., 66, 158, 271, 272
Liljefors T., 69, 272
Lipkwowitz, K. B., 270
Li, S., 272
local minimum, 175

M

Maple, J. R., 20, 27, 28, 31, 272, 273, 275
Maxwell-Boltzmann
distribution, 208
equation, 207
factor, 253
Mayo, S. L., 22, 51, 68, 273
McCammon, J. A., 176, 230, 272, 273, 275
McGuire, R. F., 273
McQuarrie, 216, 273
methanol, 251
Mezei, M., 176, 247, 273
Mezei's algorithm, 247
Miller, G. W., 66, 273
minimization, 149
algorithms, 151, 172
constraints, 98
convergence, 173, 174, 175
derivatives, 152, 174
efficiency, 151
energy expression, 151
energy zero, arbitrary, 176
initial relaxation, 159
iteration, defined, 156
line search, 153, 154
progressive, 99
restraints, 98
setting up, 169
significance, 176
strategies, 151, 169
system size, 161, 163
uses, 2
minimizers
advantages, 165, 166
Broyden-Fletcher-Goldfarb-Shanno, 165
comparative efficiency, 168
conjugate gradients, 160, 173
Davidon-Fletcher-Powell, 165
differences among Newton methods, 164
discontinuities in potential energy surface, sensitivities to, 135
limitations, 163
Newton-Raphson, 162, 163, 173
Newton-Raphson, algorithm, 164
quasi-Newton-Raphson, 164
steepest descents, 157, 159
truncated Newton-Raphson, 166
minimum image model, 115, 221
MMFF
availability, 26
energy expression, 33
modeling incomplete systems, 99
molecular dynamics, see dynamics
molecular mechanics, 12
molecular modeling program, difinition, 5
Momany, F. A., 22, 55, 67, 273
monomer definitions, 74
Montgomery, 269
Morphology/Lifson forcefield, 66
Morphology/Momany forcefield, 67
Morphology/Scheraga forcefields, 67
Morphology/Williams forcefield, 67
Morse potential, 58, 173
harmonic potential, compared with, 59
MSI's website, 6, 123
MSXX, 63
Morse functional form, 64
parameterization, 63
Mumby, S. J., 275
Murcko, M. A., 54, 276

N

Nachbar, R. B., 21, 34, 271
Naider, F., 271
natural response functions, 206
neighbor list, 132
Némethy, G., 67, 273
Newsam, J. M., 270
Newton's equation of motion, 11, 188
Nguyen, D. T., 276
NMR relaxation times, 234
nonbond interactions, 59
cell multipole method, 136
cutoff distance and, 126, 127
definition, 18
Ewald calculations, 141
system size and, 125
nonbond list, 132
nonbond terms, 16
non-hypervalent, 48
nonpolar hydrogens, 53
Norgett, M. J., 145, 270
normal mode analysis, 175
Nosé, S., 213, 215, 273
Nowak, A. K., 273, 276
nuclear motion equation, 11
nucleic acids, 52
number density, 234

O

off-diagonal terms, see cross terms
Olafson, B. D., 269, 273
oligosaccharides, 54
Oppenheimer, J. R., 11, 269
Osguthorpe, D. J., 270

P

Parrinello, M., 205, 224, 273
partition function, 255
peptides, 23
periodic boundary conditions, 220, 221
definition, 111
periodic systems
disordered, 135
dynamics, 204, 205, 218, 220
Ewald calculations, 141
Peterson, B. K., 273
Pettitt, B., 269
Pickett, S. D., 66, 273
polymer forcefield, 61
polymers, 52
polysaccharides, 53, 54
polyvinylidene fluoride forcefield, 60, 63
Postma, J. P. M., 269, 275
Post, M. F. M., 273
potential energy surface, 10, 11, 16
discontinuities, 135
empirical fit, 11, 12
non-quadratic, 173
saddle points, 182
shape of, 179
transition states, 182
water molecule, 17
Potentials Forcefield, 79, 81
Pottle, M. S., 273
Powell, M. J. D., 161, 274
pressure, 206
and correct statistical ensemble, 221
calculation, 218
changing, 222
control, 221
functional form, 216
periodic boundary conditions, 218
sign conventions, 218
thermodynamic, 218
units, 217
virial theorem, 218
Press, W. H., 174, 193, 250, 274
Profeta, S. Jr., 276
proteins, 23, 52
protonated amines, 134
p1_4 parameter, 121

Q

quantum effects, 176
quantum mechanical probability function, 14
quartz, 142
Quirke, N., 176, 274

R

radius of gyration, 234
Rahman, A., 224, 273
Rappé, A. K., 21, 41, 42, 43, 81, 269, 270, 274
rattle command, 107
Ravimohan, C., 251
Ray, J. R., 203, 206, 274
reading models, 74
Reeves, C. M., 161, 270
Ree, F. H., 258
Reidl, D., 112, 274
relative free energy
benchmark calculation, 251
convergence, 250, 253
degrees of freedom, 252
drift, 254
example, 251
FDTI, 247, 249, 250
finite difference thermodynamic integration, see FDTI
functional form, 250
perturbation method, 248
results, 253
setting up, 252
thermodynamic cycle, 251
residue definitions, 74
restraints, 16, 150
angle, 108
definition, 15, 96
distance, 104
dynamics, 231
inversion, 110
torsion, 108
Rigby, D., 33, 274, 275
RNA, 23
Roberts, V. A., 270
Rokhlin, V. I., 136, 140, 270
Rone, R., 22, 55, 273
Rosenthal, A. B., 61, 274
rotational barriers, heights, 178
Runge-Kutta integrator, 193
Ryckaert, J.-P., 232, 274

S

saddle points, 174
Sauer, J., 20, 32, 271
Scale_Terms Parameters, 121
Scheraga, H. A., 273
Schmidt, K. E., 136, 140, 274
Schrödinger equation, 10
Set Parameters, 125
setting up calculations, 75
Sharon, R., 271
shear stress, 217
shielded dielectric function, 124
Shi, S., 275
simulated annealing, 228
simulation engine, definition, 4
Singh, U. C., 176, 251, 275, 276
Sinha, S. K., 270
Skiff, W. M., 274
small molecules, 52
Smit, B., 273
solvent, 111, 113
Sorption Demontis forcefield, 66
Sorption Pickett forcefield, 66
Sorption Yashonath forcefield, 66
Soules, T. F., 61, 275
special-purpose forcefields
availability, 60
characteristics, 61
specific heat, 206, 207, 236
specific heat at constant pressure, 206
spectral densities, 234
spline switching nonbond cutoff, 131
Sprague, J. T., 69, 275
Stapleton M. R., 276
States, D. J., 269
statistical ensembles, 187, 201
Stern, P. S., 271
Stockfisch, T. P., 272, 273
Straatsma, T. P., 176, 275
stress, 217, 224, 225
control, 221
sign conventions, 218
tensor components, 204
units, 217
stress-strain relationship, 205, 217, 224
structural similarities, 229
Sun, H., 20, 32, 33, 274, 275
surface charges, 146
Sussman, F., 276
Swaminathan, S., 269
Swift, J. F. P., 273
switching atom defined, 133
switching function, effect on nonbond energy, 130
symmetry relations, 117

T

Tai, J. C., 272, 275
Tembe, B. L., 176, 275
temperature, 207
and average kinetic energy, 208
and correct statistical ensemble, 210
calculation of, 209
control, 216
damping, 213
distribution of atomic velocities, 207
integration errors, 199
nonperiodic system, 209
nonzero, 185
periodic system, 209
template atoms, 101
template forcing, 101, 151
functional forms, 101
tensile stress, 217
Tesar, A. A., 61, 275
tethering, 99, 103
functional forms, 103
Teukolsky, S. A., 274
Thacher, T. S., 273
thermal expansion, 206, 207
thermodynamic cycle, 176
thermodynamic ensembles, 187
thermodynamic response function, 203
thermodynamic temperature, 209
Thomas, J. M., 273, 276
Tildesley, D. J., 114, 206, 218, 223, 269
timestep length in dynamics, 193
Tolleanaere, J. P., 260
torsions
forcing, 108
restraints, 108, 109
trajectory
animation, 234
contents, 234
definition, 189
length, 237
uses, 234
transition states, 179

U

united-atom representation, 53
Universal forcefield
atom type naming, 42
availability, 35
characteristics, 21
charges, 43
implementation, 41
parameter generation, 42
versions, 43

V

VALBOND
characteristics, 21
valence exclusions, 121
valence interactions, 16
van Beest, B. W. H., 64, 275
van der Waals
combination rules, 122
cutoff distance and, 127, 128
Ewald calculations, 142
interaction potential, 195
interactions, 28, 53, 59
van Gunsteren, W. F., 269
van Santen, R. A., 275
Varshneya, A. K., 61, 275
Verlet leapfrog integrator, 190, 191
Verlet velocity integrator, 190, 191
compared with ABM4 integrator, 200
Verlet, L., 191, 276
Vetterling, W. T., 274
vibrational calculations, 181
computational costs, 183
cross terms and, 183
entropy, 183
forcefield accuracy and, 183
free energy, 178
frequencies, 59, 163, 178, 181
from potential energy surface, 180
harmonic, 149
imaginary frequencies, 182
normal mode analysis, 163
prerequisites, 181
quality, 181
quantum mechanical equation, 182
uses, 178
virial, 206
viscous fluids, 230
volume, periodic boundary conditions, 218

W

Waldman, M., 20, 123, 272, 276
Warshel, A., 176, 272, 276
Watanabe-Austin forcefield, 66
Watanabe, K., 66, 276
water, 56
constrained, 233
fixed-geometry model, 107, 233
SPC, 107, 233
TIP3P, 107, 233
Weiner, P., 276
Weiner, S. J., 22, 52, 69, 276, 284
Wiberg, K. B., 54, 276
Williams, D. E., 67, 276
Wilson, E. B., 28, 179, 276
Wolff, J., 270
Wolynes, P. G., 273
Woodcock, L. V., 61, 276

Y

Yang, Y., 275
Yan, L., 275
Yashonath, S., 66, 270, 276
Yuh, Y., 275

Z

zeolite forcefield, 60, 61
zero-point corrections, 176, 178, 182
Zirl, D. M., 61, 270, 276


Last updated September 10, 1998.
Copyright © 1997, 1998 Molecular Simulations Inc. All rights reserved.