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General Features
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orac-manual
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Fast switching Double Annihilation
Contents
Index
Input to ORAC
Subsections
General Features
Input File.
Instructions Set.
Handling External Files.
Environments, Commands and Sub-commands
Commands' supporting policy.
&ANALYSIS
START
STOP
UPDATE
&INOUT
ASCII
ASCII_OUTBOX
DCD
DYNAMIC
DUMP
PLOT
RESTART
TRAJECTORY
&INTEGRATOR
MTS_RESPA
TIMESTEP
&META
ADD_BOND
ADD_BEND
ADD_TORS
RATE
READ
TEMPERED
WTEMPERED
SAVE
&PARAMETERS
ADD_TPG SOLUTE
JOIN
PRINT_TOPOLOGY
READ_TPGPRM
READ_PRM_ASCII
READ_TPG_ASCII
REPL_RESIDUE
WRITE_TPGPRM_BIN
&POTENTIAL
ADD_STR_BONDS
ADD_STR_BENDS
ADD_STR_COM
ADD_STR_TORS
ADJUST_BONDS
AUTO_DIHEDRAL
BENDING
CHECK_COORD_OFF
CONSTRAINT
CUTOFF
DEFINE_ALCHEMICAL_ATOM
ERF_CORR
ERFC_SPLINE
EWALD
GROUP_CUTOFF
H-MASS
I-TORSION
INTRAMOL
JORGENSEN
KEEP_BONDS
LJ-FUDGE
LINKED_CELL
QQ-FUDGE
SELECT_DIHEDRAL
SHIFT-POT
SOFT-CORE
STEER_PATH
STRETCHING
UPDATE
VERLET_LIST
&PROPERTIES
DEF_FRAGMENT
DIST_FRAGMENT
FORCE_FIELD
GOFR
HBONDS
PRINT_DIPOLE
STRUCTURES
TIME_CORRELATIONS
VORONOI
WRITE_GYR
&REM
BATTERIES
PRINT
PRINT_DIAGNOSTIC
PRINT_ENERGY
SEGMENT
SETUP
SKIP_FORCE
STEP
&RUN
CONTROL
DEBUG
MAXRUN
PRINT
PROPERTY
REJECT
SCALE_MASS
STEER
TIME
&SETUP
CHANGE_CELL
CRYSTAL
READ_PDB
REPLICATE
RESET_CM
READ_CO
SOLUTE
SOLVENT
TEMPLATE
&SGE
FIX_FREE_ENERGY
PRINT_ACCEPTANCE_RATIO
PRINT_WHAM
SEGMENT
SETUP
STEP
TRANSITION_SCHEME
ZERO_FREE_ENERGY
&SIMULATION
ANDERSEN
ANNEALING
BUSSI
ISEED
ISOSTRES
ISOSTRESSXY
FREQUENCIES
MINIMIZE
MDSIM
SCALE
SCALING
STRESS
TEMPERATURE
THERMOS
WRITE_PRESSURE
&SOLUTE
COORDINATES
DEF_SOLUTE
SCALE_CHARGES
SPACE_GROUP
&SOLVENT
ADD_UNITS
CELL
COORDINATES
GENERATE
INSERT
READ_SOLVENT
REDEFINE
Input to
ORAC
: Force Field and Topology Files
Force Field Parameters
BENDING
BOND
NONBONDED
TORSION PROPER
TORSION IMPROPER
Topology
RESIDUE
atoms
rigid
bonds
omit_angles
dihed
imphd
backbone
termatom
acc
don
