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Index

$\alpha $-carbon
STRUCTURES
acc
acc
acceptance ratio
ADD_BOND | ADD_BEND | ADD_TORS | PRINT
ADD_TORS
ADD_TORS
ADD_BEND
ADD_BEND
ADD_BOND
ADD_BOND
ADD_STR_BENDS
ADD_STR_BENDS
ADD_STR_BONDS
ADD_STR_BONDS
ADD_STR_TORS
ADD_STR_TORS
adding a bending
ADD_STR_BONDS
adding a harmonic distance constraint
&POTENTIAL
adding an harmonic torsion
ADD_STR_BENDS
ADD_TPG SOLUTE
ADD_TPG SOLUTE
ADD_UNITS
ADD_UNITS
ADJUST_BONDS
ADJUST_BONDS
alkanes
Applications
AMBER force field
Subdivision of the ``Bonded''
&ANALYSIS
&ANALYSIS
ANDERSEN
ANDERSEN
Andersen, H.C.
ANDERSEN
angular_cutoff
HBONDS
angular cutoff
HBONDS
animation
using ORAC generated file
PLOT
animation from xyz file
DEF_FRAGMENT
ANNEALING
UPDATE | ANNEALING
ASCII
ASCII | ASCII_OUTBOX
asymmetric unit
SPACE_GROUP
atom_record
DUMP
atomic charges
subtracting excess charge
DEF_SOLUTE
atomic scaling
Equivalence of Atomic and | SCALING
Liouvillean split for
Liouvillean Split and Multiple
atoms
atoms
AUTO_DIHEDRAL
AUTO_DIHEDRAL
average
GOFR
averaged
STRUCTURES
B-spline interpolation
The smooth particle mesh
backbone
STRUCTURES | backbone
writing the coordinates of [] atoms
PLOT
barostat
The Parrinello-Rahman-Nosé Extended Lagrangian
BENDING
BENDING
printing out
PRINT_TOPOLOGY
bending potential
Subdivision of the ``Bonded'' | DEBUG
BENDINGS
BENDING
Bennett acceptance ratio
Analysis of the REM | Determination of the potential
Berendsen H.
Equivalence of Atomic and
Berne B. J
Multiple time steps integration
BOND
BOND
bonded potential
Multiple Time Steps Algorithms
subdivision of
Multiple Time Steps Algorithms
bonds
bonds
BPTI
Group Scaling and Molecular
B-spline
of the direct lattice potential
ERFC_SPLINE
canonical transformations
Canonical Transformation and Symplectic
center of mass
REPLICATE
CG
MINIMIZE
CHANGE_CELL
CHANGE_CELL
Ciccotti G.
Equivalence of Atomic and
cofm
THERMOS
compiling ORAC 
Serial version
compute accessibility
VORONOI
compute contac_solute
VORONOI
compute neighbors
VORONOI
compute volume
VORONOI
config.h file
How to set dimensions | How to set dimensions
configure file
How to set dimensions
conjugate gradient
MINIMIZE | THERMOS
constant pressure
scaling
SCALING
constant pressure simulation
Multiple Time Steps Algorithms
constant temperature simulation
Multiple Time Steps Algorithms | THERMOS | THERMOS
CONSTRAINT
CONSTRAINT
constraints
ADD_STR_TORS | BENDING
printing out
PRINT_TOPOLOGY
with r-RESPA
Potential Subdivision and Multiple
CONTROL
CONTROL
COORDINATES
COORDINATES | COORDINATES
of the solvent
ADD_UNITS | READ_SOLVENT
Crooks theorem
Steered Molecular Dynamics
CRYSTAL
CRYSTAL
crystal structure
READ_PDB
crystal symmetry
SPACE_GROUP
crystal to orthogonal matrix
READ_CO
crystallographic parameters
CHANGE_CELL
cutoff
Multiple time steps integration | The smooth particle mesh | Subdivision the Non Bonded | Subdivision the Non Bonded | Subdivision the Non Bonded | CUTOFF | ERFC_SPLINE | GOFR | VORONOI
for hydrogen bonds
HBONDS
in the reciprocal lattice
Electrostatic Corrections for the
reciprocal lattice
ERFC_SPLINE
DEBUG
DEBUG
decaalanine
Enhanced sampling in atomistic
defaults
THERMOS
DEF_FRAGMENT
DEF_FRAGMENT
DEF_SOLUTE
DEF_SOLUTE
density of states
Subdivision of the ``Bonded''
dielectric constant
Multiple time steps integration | Electrostatic Corrections for the | PRINT_DIPOLE
diffusion
TIME_CORRELATIONS
diffusion coefficient
&PROPERTIES
dihed
dihed
dihedral angle
Subdivision of the ``Bonded''
dihedral angle in torsions
Topology
dimensions
changing the, in ORAC 
How to set dimensions
dipole
&PROPERTIES
direct lattice potential
The smooth particle mesh
direct potential
subdivision of
Subdivision the Non Bonded
dirty
MTS_RESPA
discrete time propagator
Liouville Formalism: a Tool | Liouville Formalism: a Tool | Potential Subdivision and Multiple | Subdivision the Non Bonded
DIST_FRAGMENT
DEF_FRAGMENT | DIST_FRAGMENT
dist_max
FREQUENCIES
dived_step
TIME_CORRELATIONS
don
don
driven thermal changes
PLOT | STEER
driving external potential
&POTENTIAL
DUMP
DUMP
dumping the restart file
RESTART
DYNAMIC
DYNAMIC
dynamical matrix
FREQUENCIES
eigenvectors
FREQUENCIES | FREQUENCIES
electrostatic correction
ERFC_SPLINE
electrostatic corrections
Subdivision the Non Bonded
electrostatic potential
The smooth particle mesh
subdivision of
Subdivision the Non Bonded
energy equipartition
THERMOS
energy_then_die
MTS_RESPA
enhanced sampling
Multiple time steps integration
equations of motion
Canonical Transformation and Symplectic
for Parrinello-Rahman-Nosé Hamiltonian
The Parrinello-Rahman-Nosé Hamiltonian and
equilibration
TIME
ERF_CORR
ERF_CORR
ERFC_SPLINE
ERFC_SPLINE
error function
The smooth particle mesh | ERFC_SPLINE
EWALD
EWALD
Ewald method
Multiple time steps integration | The smooth particle mesh
electrostatic corrections
Subdivision the Non Bonded
in multiple time scales integrators
MTS_RESPA
intramolecular correction
ERF_CORR
intramolecular self term
The smooth particle mesh
self energy
Electrostatic Corrections for the
setting work array dimensions
How to set dimensions
smooth particle mesh
The smooth particle mesh
excess charge
DEF_SOLUTE
extended Lagrangian
Multiple Time Steps Algorithms
fluctuation theorem
The Crooks theorem
force breakup
Potential Subdivision and Multiple
force field
Subdivision of the ``Bonded'' | Input to ORAC : Force
input parameters from ASCII file
READ_PRM_ASCII
input parameters from binary file
READ_TPGPRM
force field printout
DYNAMIC
FORCE_FIELD
FORCE_FIELD
fractional translations
SPACE_GROUP
fragment
writing coordinates of
PLOT
free energy
Enhanced sampling in atomistic
FREQUENCIES
FREQUENCIES
fudge factor
LJ-FUDGE
GENERATE
GENERATE
glycine
REPL_RESIDUE
GOFR
GOFR
group scaling
The Parrinello-Rahman-Nosé Hamiltonian and | Equivalence of Atomic and | Liouvillean Split and Multiple | SCALING
Liouvillean split for
Liouvillean Split and Multiple
GROUP_CUTOFF
GROUP_CUTOFF
Hamilton
equations
Canonical Transformation and Symplectic | Liouville Formalism: a Tool
harmonic constraints
&POTENTIAL | ADD_STR_BONDS
harmonic frequencies
FREQUENCIES
HBONDS
HBONDS
heavy_atoms
VORONOI
Hermitian operator
Liouville Formalism: a Tool
histogram
HBONDS
history file
DUMP | DUMP | TRAJECTORY | &PROPERTIES
auxiliary file
DUMP
H-MASS
H-MASS
hydrogen bond
HBONDS | acc
acceptor and donor
don
imphd
imphd
improper torsion
Subdivision of the ``Bonded'' | PRINT_TOPOLOGY | DEBUG | imphd
definition of, in the parameter file
TORSION IMPROPER
&INOUT
&INOUT
INSERT
INSERT
inst_xrms
STRUCTURES
&INTEGRATOR
&INTEGRATOR
reversible
Liouville Formalism: a Tool
symplectic
Enhanced sampling in atomistic | Liouville Formalism: a Tool
interchange matrix
SPACE_GROUP
ISEED
ISEED
ISOSTRESS
ISOSTRESS
isothermal-isobaric ensemble
Applications
I-TORSION
I-TORSION
jacobian
Canonical Transformation and Symplectic
Jarzynski identity
The Crooks theorem
JOIN
JOIN
JORGENSEN
JORGENSEN
KEEP_BONDS
KEEP_BONDS
k-ewald
MTS_RESPA
leap frog algorithm
Liouville Formalism: a Tool
Legendre transformation
The Parrinello-Rahman-Nosé Hamiltonian and
Lennard-Jones
Applications | NONBONDED
cutoff
Subdivision the Non Bonded
parameters
NONBONDED
linked cell
LINKED_CELL | UPDATE
LINKED_CELL
LINKED_CELL
Liouville
formalism
Liouville Formalism: a Tool
Liouvillean
Multiple time steps integration | Potential Subdivision and Multiple | Subdivision the Non Bonded
split of Parrinello-Rahman-Nosé
Equivalence of Atomic and
liquid water
Electrostatic Corrections for the
LJ-FUDGE
LJ-FUDGE
Lucy's functions
Implementation in ORAC 
lysozyme
JOIN
Markovian process
Steered Molecular Dynamics
Martyna G
Multiple time steps integration
mass
of the Nosé thermostat
THERMOS
specifying the type atomic
NONBONDED
maximum likelihood
Determination of the potential
MAXRUN
MAXRUN
MDSIM
MDSIM
mean square displacement
TIME_CORRELATIONS
memory demand in ORAC
How to set dimensions
Message Passing library interface
Serial version
&META
&META
metadynamics
Enhanced sampling in atomistic | Metadynamics Simulation: history-dependent algorithms | ADD_BOND | ADD_BEND | ADD_TORS
Gaussian and Lucy's function
Implementation in ORAC 
multiple walkers
Enhanced sampling in atomistic
well-tempered metadynamics
Implementation in ORAC 
MINIMIZE
MINIMIZE
mixing rules
NONBONDED
molecular scaling
Liouvillean Split and Multiple | Group Scaling and Molecular | SCALING
Liouvillean split for
Liouvillean Split and Multiple
MPI
Serial version
MTS_RESPA
MTS_RESPA
multiple Bennett acceptance ratio
Analysis of the REM
multiple restarts in parallel simulation
RESTART
multiple time steps
Multiple time steps integration | Switching to Other Ensembles
for Parrinello-Rahman-Nosé Hamiltonian
The Parrinello-Rahman-Nosé Hamiltonian and
neighbor list
LINKED_CELL | UPDATE
for hydrogen bonds
HBONDS
setting work arrays dimensions
How to set dimensions
non bonded potential
subdivision of
The smooth particle mesh
non-bonded potential
Multiple Time Steps Algorithms
Nosé thermostat
The Parrinello-Rahman-Nosé Extended Lagrangian | THERMOS | THERMOS
no_step
FREQUENCIES
NPT ensemble
Multiple Time Steps Algorithms | THERMOS
NVT ensemble
Multiple Time Steps Algorithms | Multiple Time Steps Algorithms | Group Scaling and Molecular | PLOT | THERMOS
occupy
DUMP
omit_angles
omit_angles
Open MPI
Serial version
pair correlation function
GOFR
parallel version
compiling
Parallel version
REM algorithm
SETUP
steered molecular dynamics simulations
ADD_STR_BONDS
&PARAMETERS
&PARAMETERS
Parrinello-Rahman-Nosé Extended Lagrangian
Multiple Time Steps Algorithms
PARXXXX directories
SETUP | Parallel version
PDB
READ_PDB | SOLVENT
generating a file
ASCII | ASCII_OUTBOX
writing the [] file to disk
PLOT
PLOT
PLOT
PLOT FRAGMENT
DEF_FRAGMENT | DIST_FRAGMENT
PMF
Steered Molecular Dynamics
position Verlet
Liouville Formalism: a Tool
&POTENTIAL
&POTENTIAL
bending
Subdivision of the ``Bonded''
bonded
Multiple Time Steps Algorithms
non-bonded
Multiple Time Steps Algorithms
of mean force
Steered Molecular Dynamics
stretching
Subdivision of the ``Bonded''
subdivision of
Potential Subdivision and Multiple
potential of mean force
determination of via the Crooks theorem
Determination of the potential
potential subdivision
Multiple Time Steps Algorithms | Subdivision the Non Bonded
for the AMBER force field
Subdivision of the ``Bonded'' | Subdivision the Non Bonded
PRESSURE
parameter in the config.h file
How to set dimensions
print
HBONDS | PRINT
for harmonic calculations
FREQUENCIES
replica exchange method
PRINT
PRINT_DIPOLE
PRINT_DIPOLE
print_histo
HBONDS
printing the force field parameters
DYNAMIC | DEBUG
printing topology information
DEBUG
PRINT_TOPOLOGY
PRINT_TOPOLOGY
print_xyz_only
print_xyz_only
propagator
Liouville Formalism: a Tool
discrete time
Liouville Formalism: a Tool
stepwise
Liouville Formalism: a Tool
proper torsion
Subdivision of the ``Bonded'' | PRINT_TOPOLOGY | DEBUG
definition of, in the parameter file
TORSION PROPER
frequency range
Subdivision of the ``Bonded''
&PROPERTIES
&PROPERTIES
PROPERTY
PROPERTY
protein
printing out the sequence
PRINT_TOPOLOGY
giving the input sequence in ORAC 
JOIN
p_test
MTS_RESPA
QQ-FUDGE
QQ-FUDGE
r-RESPA
Potential Subdivision and Multiple
energy conservation
Applications | Applications
for NPT ensemble
Equivalence of Atomic and
input examples
MTS_RESPA
performances
Applications | Applications
use in ORAC
MTS_RESPA
with Parrinello-Rahman-Nosé Hamiltonian
The Parrinello-Rahman-Nosé Hamiltonian and
radial_cutoff
HBONDS
radial distribution function
&PROPERTIES
RATE
RATE
RATTLE
Constraints and r-RESPA
reaction coordinate
Enhanced sampling in atomistic | The Crooks theorem
reaction field
Multiple time steps integration
READ
READ
READ_CO
READ_CO
reading the restart file
RESTART | CONTROL
READ_PDB
READ_PDB
READ_PRM_ASCII
READ_PRM_ASCII
READ_SOLVENT
READ_SOLVENT
READ_TPG_ASCII
READ_TPG_ASCII
READ_TPGPRM
READ_TPGPRM
reciprocal lattice
Subdivision the Non Bonded
reciprocal lattice potential
The smooth particle mesh
REDEFINE
REDEFINE
reference system
Potential Subdivision and Multiple | Subdivision the Non Bonded
REJECT
REJECT
&REM
&REM
REMSTEP
REMSTEP
replica exchange method
Electrostatic Corrections for the | PRINT | SETUP
Hamiltonian REM
Hamiltonian REM
local scaling and global scaling
SETUP
temperature REM
Temperature REM
REPLICATE
REPLICATE
REPL_RESIDUE
REPL_RESIDUE
RESET_CM
RESET_CM
RESIDUE
REPL_RESIDUE | HBONDS | RESIDUE | RESIDUE
definition of, in the tpg file
RESIDUE
sequence
JOIN
residue sequence
DEBUG
RESTART
RESTART | CONTROL
restart file
RESTART | CONTROL | CHANGE_CELL
parallel simulation
RESTART
restricted canonical transformation
Canonical Transformation and Symplectic
reversible integrator
Liouville Formalism: a Tool
rigid
rigid
root mean square displacement
HBONDS | STRUCTURES | TEMPLATE | DEF_SOLUTE
&RUN
&RUN
Ryckaert J.-P.
Equivalence of Atomic and
SAVE
SAVE
saving coordinates to disk
DUMP
SCALING
SCALE | SCALING
SCALE_CHARGES
SCALE_CHARGES
scaling
equivalence of atomic and group
Equivalence of Atomic and
scaling method
for constant pressure simulation
SCALING
SD
MINIMIZE
SEGMENT
SEGMENT
SELECT_DIHEDRAL
SELECT_DIHEDRAL
&SETUP
&SETUP
replica exchange method
SETUP
SHAKE
Multiple time steps integration | Constraints and r-RESPA | BENDING
&SIMULATION
&SIMULATION
simulation box
&SETUP
smooth particle mesh Ewald (see also SPME)
The smooth particle mesh
&SOLUTE
SOLUTE | &SOLUTE
defining a fragment of
&PROPERTIES | DEF_FRAGMENT
input examples
READ_CO
input topology from ASCII file
READ_TPG_ASCII
input topology from binary file
READ_TPGPRM
inserting in solvent
INSERT
pair correlation function
GOFR
setting up the unit cell
COORDINATES
thermostatting solute atoms
THERMOS
thermostatting solvent atoms
THERMOS
topology
CRYSTAL
total charge
DEF_SOLUTE
solute tempering
SEGMENT
&SOLVENT
SOLVENT | &SOLVENT
generating the coordinates
COORDINATES | COORDINATES | GENERATE
input examples
SOLUTE
reading the coordinates of
ADD_UNITS | READ_SOLVENT
setting up the unit cell
COORDINATES | GENERATE
space group
READ_PDB | COORDINATES | SPACE_GROUP
SPACE_GROUP
SPACE_GROUP
spherical cutoff
Subdivision the Non Bonded
SPME
Multiple time steps integration | Subdivision of the ``Bonded'' | The smooth particle mesh | EWALD
accuracy
The smooth particle mesh
B-spline interpolation
The smooth particle mesh
in multiple time scales integrators
MTS_RESPA
memory demand
The smooth particle mesh
performances
The smooth particle mesh
setting work arrays dimensions.
How to set dimensions
STOP
START | STOP
steepest descent
MINIMIZE
STEER
STEER
steered molecular dynamics
Enhanced sampling in atomistic | Steered Molecular Dynamics
adding a time dependent bending
ADD_STR_BONDS
adding a time dependent stretching
&POTENTIAL
adding a time dependent torsion
ADD_STR_BENDS
along a curvilinear coordinate
SELECT_DIHEDRAL
printing out the work
PLOT
restart
STEER
thermal changes
PLOT
STEER_PATH
STEER_PATH
step
MTS_RESPA
s_test
MTS_RESPA
STRESS
STRESS
STRETCHING
BOND
for the solute
STRETCHING
printing out
PRINT_TOPOLOGY
stretching potential
Subdivision of the ``Bonded'' | DEBUG
structure factor
The smooth particle mesh | &PROPERTIES | GOFR | TIME_CORRELATIONS
structured commands
definition of
Input File.
VORONOI
STRUCTURES | VORONOI
symplectic
building integrators
Liouville Formalism: a Tool
condition
Liouville Formalism: a Tool
condition for canonical transformations
Canonical Transformation and Symplectic
integrators
Enhanced sampling in atomistic
notation of the equations of motion
Canonical Transformation and Symplectic
TEMPERATURE
TEMPERATURE
temperature scaling
with Nosé thermostats
THERMOS
TEMPERED
TEMPERED
TEMPLATE
TEMPLATE
termatom
termatom
test-times
MTS_RESPA
thermal changes
STEER
thermal work
STEER
thermalization
TIME
THERMOS
THERMOS
thermostat
The Parrinello-Rahman-Nosé Extended Lagrangian | THERMOS
Andersen
ANDERSEN
TIME
TIME
time dependent bending
ADD_STR_BONDS
time dependent stretching
&POTENTIAL
time dependent torsion
ADD_STR_BENDS
TIME_CORRELATIONS
TIME_CORRELATIONS
TIMESTEP
TIMESTEP
topology
REPL_RESIDUE | Input to ORAC : Force | Topology
adding extra topology
ADD_TPG SOLUTE
from ASCII file
READ_TPG_ASCII
from binary file
READ_TPGPRM
printing
PRINT_TOPOLOGY
torsion
definition of dihedral angle
Topology
TORSION IMPROPER
TORSION IMPROPER | imphd
printing out
PRINT_TOPOLOGY
proper
TORSION PROPER
torsional potential
Applications | Subdivision of the ``Bonded'' | DEBUG
TORSION IMPROPER
TORSION IMPROPER
TORSION PROPER
TORSION PROPER | TORSION PROPER
total
HBONDS
TRAJECTORY
TRAJECTORY
trajectory file
&ANALYSIS | START | DUMP | DUMP | &PROPERTIES
auxiliary file
DUMP
unformatted xyz coordinates only
print_xyz_only
Trotter formula
Liouville Formalism: a Tool
Tuckerman M.
Multiple time steps integration
unformatted trajectory files
print_xyz_only
unit cell
COORDINATES | COORDINATES | GENERATE
replicating along selected directions
READ_PDB | COORDINATES | COORDINATES
unitary transformation
Liouville Formalism: a Tool
UPDATE
UPDATE
use_neighbor
GOFR
use_neighbors
for hydrogen bonds
HBONDS
vacf
TIME_CORRELATIONS
valine
RESIDUE
velocity
rescaling
SCALE
velocity autocorrelation function
&PROPERTIES | TIME_CORRELATIONS
velocity Verlet
Liouville Formalism: a Tool
Verlet
neighbor list
VERLET_LIST
VERLET_LIST
VERLET_LIST
very_cold_start
MTS_RESPA
virtual variables
The Parrinello-Rahman-Nosé Hamiltonian and
Volume calculation
VORONOI
Voronoi
Group Scaling and Molecular
Voronoi Polihedra
VORONOI
Wang-Landau algorithm
Metadynamics Simulation: history-dependent algorithms
water
Group Scaling and Molecular
properties of
Electrostatic Corrections for the
work
in a SMD simulation
PLOT
write
DUMP
WRITE_GRADIENT
MINIMIZE
WRITE_GYR
WRITE_GYR
WRITE_PRESSURE
WRITE_PRESSURE
WRITE_TPGPRM_BIN
WRITE_TPGPRM_BIN
WTEMPERED
WTEMPERED
Xmol animation
DEF_FRAGMENT
X_RMS
DEF_SOLUTE
xyz format
PLOT