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Index

.vmdrc
Hot Keys
.vmdrc
.vmdrc and vmd.rc Files
vmd.rc
.vmdrc and vmd.rc Files
.mailcap
Setting up your .mailcap
.vmdsensors
Configuring input devices
.vmdrc
Using text commands
vmd.rc
Using text commands
ACTC
Copyright and Disclaimer Notices
AMBER
files
Loading A Molecule | Reading Trajectory Frames
Ambient Occlusion
Display Menu and Display
ambient occlusion lighting
display | render
analysis
scripting
Using the atomselect command
speed
Using the atomselect command
angles
Label categories
animate
command
Tcl Text Commands | Tcl Text Commands
Python module
animate
window controls
Main Window Animation Controls
animation
A Quick Animation
appending
Reading Trajectory Frames
delete
Deleting Trajectory Frames | animate | animate
duplicate frame
animate
frames
Reading Trajectory Frames
goto end
animate
goto start
animate
hot keys
Hot Keys
jump
Jumping to Specific Frames | animate
movie
Making a Movie
play
animate
read
Reading Trajectory Frames | animate
smoothing
Trajectory Smoothing. | mol | molrep
speed
Animation Speed | animate
step
Animation Speed
style
animate
loop
Looping Styles
once
Looping Styles
rock
Looping Styles
write
Saving Trajectory Frames | animate
antialiasing
Display Menu and Display | display | render
atom
changing properties
Using the atomselect command
color
auto-update
mol
coordinates
rotate | scale | translate
changing
Comparing Two Structures | Using the atomselect command
min and max
Coordinate min and max
info
atomselect | Using the atomselect command
name lists
Selections Tab | Selections Tab
picking
Comparing Two Structures
selection
Viewing a molecule: Myoglobin | An Introduction to Atom | Molecular Drawing Methods | Selection Methods | atomselect | Using the atomselect command
auto-update
mol
changing properties
An atom selection example
comparison
Comparison selections
default
mol
examples
An Introduction to Atom | Selection Methods
keywords
Selections Tab | Selection Methods | Definition of Keywords and | Definition of Keywords and
logic
Short Circuiting
macros
Selections Tab | atomselect | The AtomSel class (DEPRECATED)
math functions
Definition of Keywords and
modes
Selection Methods
Python
Atom selections in Python
macros
The AtomSel class (DEPRECATED)
quoting
Quoting with Single Quotes
regular expression
Double Quotes and Regular
same
within and same
sequence
sequence
Tcl
macros
atomselect
text
Using the atomselect command
update
Finding waters near a
volumetric data
Definition of Keywords and
within
within and same
atoms
distance between
Comparing Two Structures
plotting
Plotting a label's value
atomselect
command
Tcl Text Commands | animate | Molecular Analysis | Using the atomselect command
axes
Display Menu and Display
command
Tcl Text Commands | atomselect
Python module
axes
Babel
Babel interface
backface culling
Display Menu and Display
batch mode
VMD Command-Line Options
beta values
Root mean square deviation
BioCoRE
For information on our
bonds
add or remove
Mouse Modes
determining
What happens when a
label
Label categories | Label categories
resolution
Bonds
unusual
What happens when a
cachemode
Display Menu and Display
callbacks
Python
Python callbacks
Tcl
Tcl callbacks | Tcl callbacks
center of mass
Using the atomselect command
CHARMM
files
Loading A Molecule | Reading Trajectory Frames
chemical2vmd
Setting up your .mailcap
clipping planes
Display Menu and Display
user defined
mol
collective variables
global
analysis
Configuration syntax for the
colvar
name
General options for a
colvar
width
General options for a
colvar
lowerBoundary
General options for a
colvar
upperBoundary
General options for a
colvar
hardLowerBoundary
General options for a
colvar
hardUpperBoundary
General options for a
colvar
expandBoundaries
General options for a
colvar
subtractAppliedForce
General options for a
colvar
lowerWallConstant
Artificial boundary potentials (walls)
colvar
lowerWall
Artificial boundary potentials (walls)
colvar
upperWallConstant
Artificial boundary potentials (walls)
colvar
upperWall
Artificial boundary potentials (walls)
colvar
outputValue
Trajectory output
colvar
outputVelocity
Trajectory output
colvar
outputEnergy
Trajectory output
colvar
outputTotalForce
Trajectory output
colvar
outputAppliedForce
Trajectory output
colvar
extendedLagrangian
Extended Lagrangian.
colvar
extendedFluctuation
Extended Lagrangian.
colvar
extendedTimeConstant
Extended Lagrangian.
colvar
extendedTemp
Extended Lagrangian.
colvar
extendedLangevinDamping
Extended Lagrangian.
colvar
corrFunc
Statistical analysis of collective
colvar
corrFuncWithColvar
Statistical analysis of collective
colvar
corrFuncType
Statistical analysis of collective
colvar
corrFuncNormalize
Statistical analysis of collective
colvar
corrFuncLength
Statistical analysis of collective
colvar
corrFuncStride
Statistical analysis of collective
colvar
corrFuncOffset
Statistical analysis of collective
colvar
corrFuncOutputFile
Statistical analysis of collective
colvar
runAve
Statistical analysis of collective
colvar
runAveLength
Statistical analysis of collective
colvar
runAveStride
Statistical analysis of collective
colvar
runAveOutputFile
Statistical analysis of collective
atom group
atomNumbers
Selection keywords
atom group
indexGroup
Selection keywords
atom group
atomNumbersRange
Selection keywords
atom group
atomNameResidueRange
Selection keywords
atom group
psfSegID
Selection keywords
atom group
atomsFile
Selection keywords
atom group
atomsCol
Selection keywords
atom group
atomsColValue
Selection keywords
atom group
dummyAtom
Selection keywords
atom group
centerReference
Moving frame of reference.
atom group
rotateReference
Moving frame of reference.
atom group
refPositions
Moving frame of reference.
atom group
refPositionsFile
Moving frame of reference.
atom group
refPositionsCol
Moving frame of reference.
atom group
refPositionsColValue
Moving frame of reference.
atom group
fittingGroup
Moving frame of reference.
atom group
enableFitGradients
Moving frame of reference.
atom group
enableForces
Moving frame of reference.
distance
group1
distance: center-of-mass distance between
distance
forceNoPBC
distance: center-of-mass distance between
angle, dipoleAngle, dihedral
oneSiteTotalForce
distance: center-of-mass distance between
distanceZ
main
distanceZ: projection of a
distanceZ
ref
distanceZ: projection of a
distanceZ
ref2
distanceZ: projection of a
distanceZ
axis
distanceZ: projection of a
distanceInv
exponent
distanceInv: mean distance between
cartesian
atoms
cartesian: vector of atomic
coordNum
cutoff
coordNum: coordination number between
coordNum
cutoff3
coordNum: coordination number between
coordNum
expNumer
coordNum: coordination number between
coordNum
expDenom
coordNum: coordination number between
coordNum
group2CenterOnly
coordNum: coordination number between
hBond
acceptor
hBond: hydrogen bond between
rmsd
atoms
rmsd: root mean square
rmsd
refPositions
rmsd: root mean square
rmsd
refPositionsFile
rmsd: root mean square
rmsd
refPositionsCol
rmsd: root mean square
rmsd
refPositionsColValue
rmsd: root mean square
eigenvector
vector
eigenvector: projection of the
eigenvector
vectorFile
eigenvector: projection of the
eigenvector
vectorCol
eigenvector: projection of the
eigenvector
vectorColValue
eigenvector: projection of the
eigenvector
differenceVector
eigenvector: projection of the
inertiaZ
axis
inertiaZ: total moment of
orientation
closestToQuaternion
orientation: orientation from reference
tilt
axis
spinAngle: angle of rotation
alpha
residueRange
alpha: $ \alpha$ -helix content
alpha
psfSegID
alpha: $ \alpha$ -helix content
alpha
hBondCoeff
alpha: $ \alpha$ -helix content
alpha
angleRef
alpha: $ \alpha$ -helix content
alpha
angleTol
alpha: $ \alpha$ -helix content
alpha
hBondCutoff
alpha: $ \alpha$ -helix content
alpha
hBondExpNumer
alpha: $ \alpha$ -helix content
alpha
hBondExpDenom
alpha: $ \alpha$ -helix content
dihedralPC
vectorFile
dihedralPC: protein dihedral pricipal
dihedralPC
vectorNumber
dihedralPC: protein dihedral pricipal
any component
name
Configuration keywords shared by
any component
scalable
Configuration keywords shared by
distanceZ
period
Periodic components.
distanceZ, dihedral or spinAngle
wrapAround
Periodic components.
any component
componentCoeff
Linear and polynomial combinations
any component
componentExp
Linear and polynomial combinations
colvar
scriptedFunction
Colvars as scripted functions
colvar
scriptedFunctionType
Colvars as scripted functions
colvar
scriptedFunctionVectorSize
Colvars as scripted functions
colvar bias
name
Biasing and analysis methods
colvar bias
colvars
Biasing and analysis methods
colvar bias
outputEnergy
Biasing and analysis methods
metadynamics
hillWeight
Metadynamics
metadynamics
newHillFrequency
Metadynamics
metadynamics
hillWidth
Metadynamics
metadynamics
writeFreeEnergyFile
Output files
metadynamics
keepFreeEnergyFiles
Output files
metadynamics
useGrids
Performance tuning
metadynamics
rebinGrids
Performance tuning
metadynamics
wellTempered
Well-tempered metadynamics
metadynamics
biasTemperature
Well-tempered metadynamics
metadynamics
multipleReplicas
Multiple-replicas metadynamics
metadynamics
replicaID
Multiple-replicas metadynamics
metadynamics
replicasRegistry
Multiple-replicas metadynamics
metadynamics
replicaUpdateFrequency
Multiple-replicas metadynamics
metadynamics
dumpPartialFreeEnergyFile
Multiple-replicas metadynamics
metadynamics
name
Compatibility and post-processing
metadynamics
keepHills
Compatibility and post-processing
metadynamics
writeHillsTrajectory
Compatibility and post-processing
harmonic
forceConstant
Harmonic restraints
harmonic
centers
Harmonic restraints
harmonic
targetCenters
Moving restraints: steered molecular
harmonic
targetNumSteps
Moving restraints: steered molecular
harmonic
outputCenters
Moving restraints: steered molecular
harmonic
outputAccumulatedWork
Moving restraints: steered molecular
harmonic
targetNumStages
Moving restraints: umbrella sampling
harmonic
targetForceConstant
Changing force constant
harmonic
targetForceExponent
Changing force constant
harmonic
targetEquilSteps
Changing force constant
harmonic
lambdaSchedule
Changing force constant
linear
forceConstant
Linear restraints
linear
centers
Linear restraints
histogram
outputFreq
Multidimensional histograms
histogram
outputFile
Multidimensional histograms
histogram
outputFileDX
Multidimensional histograms
histogram
gatherVectorColvars
Multidimensional histograms
histogram
weights
Multidimensional histograms
histogramGrid
lowerBoundaries
Grid definition for multidimensional
histogramRestraint
lowerBoundary
Probability distribution-restraints
histogramRestraint
width
Probability distribution-restraints
histogramRestraint
gaussianSigma
Probability distribution-restraints
histogramRestraint
forceConstant
Probability distribution-restraints
histogramRestraint
refHistogram
Probability distribution-restraints
histogramRestraint
refHistogramFile
Probability distribution-restraints
metadynamics
writeHistogram
Probability distribution-restraints
global
scriptedColvarForces
Scripted biases
global
scriptingAfterBiases
#1
global
colvarsTrajFrequency
Configuration syntax for the
global
colvarsTrajAppend
Configuration syntax for the
global
colvarsRestartFrequency
Configuration syntax for the
global
indexFile
Configuration syntax for the
global
smp
Configuration syntax for the
global
smp
Configuration syntax for the
abf
applyBias
Parameters for ABF
colvars
Parameters for ABF
fullSamples
Parameters for ABF
hideJacobian
Parameters for ABF
historyFreq
Parameters for ABF
inputPrefix
Parameters for ABF
maxForce
Parameters for ABF
name
Parameters for ABF
outputFreq
Parameters for ABF
updateBias
Parameters for ABF
writeCZARwindowFile
CZAR estimator of the
alb
centers
Adaptive Linear Bias/Experiment Directed
colvars
Adaptive Linear Bias/Experiment Directed
forceRange
Adaptive Linear Bias/Experiment Directed
name
Adaptive Linear Bias/Experiment Directed
rateMax
Adaptive Linear Bias/Experiment Directed
updateFrequency
Adaptive Linear Bias/Experiment Directed
angle
group1
angle: angle between three
group2
angle: angle between three
group3
angle: angle between three
oneSiteTotalForce
angle: angle between three
coordNum
group1
coordNum: coordination number between
group2
coordNum: coordination number between
dihedral
group1
dihedral: torsional angle between
group2
dihedral: torsional angle between
group3
dihedral: torsional angle between
group4
dihedral: torsional angle between
oneSiteTotalForce
dihedral: torsional angle between
dihedralPC
angleRef
dihedralPC: protein dihedral pricipal
angleTol
dihedralPC: protein dihedral pricipal
hBondCoeff
dihedralPC: protein dihedral pricipal
hBondCutoff
dihedralPC: protein dihedral pricipal
hBondExpDenom
dihedralPC: protein dihedral pricipal
hBondExpNumer
dihedralPC: protein dihedral pricipal
psfSegID
dihedralPC: protein dihedral pricipal
residueRange
dihedralPC: protein dihedral pricipal
dipoleAngle
group1
dipoleAngle: angle between two
group2
dipoleAngle: angle between two
group3
dipoleAngle: angle between two
oneSiteTotalForce
dipoleAngle: angle between two
distance
group2
distance: center-of-mass distance between
distanceDir
group1
distanceDir: distance unit vector
group2
distanceDir: distance unit vector
oneSiteTotalForce
distanceDir: distance unit vector
distanceInv
forceNoPBC
distancePairs: set of pairwise
group1
distanceInv: mean distance between | distancePairs: set of pairwise
group2
distanceInv: mean distance between | distancePairs: set of pairwise
oneSiteTotalForce
distanceInv: mean distance between
distanceVec
group1
distanceVec: distance vector between
group2
distanceVec: distance vector between
oneSiteTotalForce
distanceVec: distance vector between
distanceXY
axis
distanceXY: modulus of the
main
distanceXY: modulus of the
ref2
distanceXY: modulus of the
ref
distanceXY: modulus of the
distanceZ
forceNoPBC
distanceZ: projection of a | distanceXY: modulus of the
oneSiteTotalForce
distanceZ: projection of a | distanceXY: modulus of the
eigenvector
atoms
eigenvector: projection of the
refPositions
eigenvector: projection of the
refPositionsCol
eigenvector: projection of the
refPositionsColValue
eigenvector: projection of the
refPositionsFile
eigenvector: projection of the
gyration
atoms
gyration: radius of gyration
harmonic
colvars
Harmonic restraints
name
Harmonic restraints
outputEnergy
Harmonic restraints
hBond
cutoff
hBond: hydrogen bond between
donor
hBond: hydrogen bond between
expDenom
hBond: hydrogen bond between
expNumer
hBond: hydrogen bond between
histogram
colvars
Multidimensional histograms
name
Multidimensional histograms
histogramGrid
upperBoundaries
Grid definition for multidimensional
widths
Grid definition for multidimensional
histogramRestraint
colvars
Probability distribution-restraints
name
Probability distribution-restraints
outputEnergy
Probability distribution-restraints
upperBoundary
Probability distribution-restraints
inertia
atoms
inertia: total moment of
inertiaZ
atoms
inertiaZ: total moment of
linear
colvars
Linear restraints
name
Linear restraints
metadynamics
colvars
Metadynamics
name
Metadynamics
outputEnergy
Metadynamics
orientation
atoms
orientation: orientation from reference
refPositions
orientation: orientation from reference
refPositionsCol
orientation: orientation from reference
refPositionsColValue
orientation: orientation from reference
refPositionsFile
orientation: orientation from reference
orientationAngle
atoms
orientationAngle: angle of rotation
refPositions
orientationAngle: angle of rotation
refPositionsCol
orientationAngle: angle of rotation
refPositionsColValue
orientationAngle: angle of rotation
refPositionsFile
orientationAngle: angle of rotation
orientationProj
atoms
orientationProj: cosine of the
refPositions
orientationProj: cosine of the
refPositionsCol
orientationProj: cosine of the
refPositionsColValue
orientationProj: cosine of the
refPositionsFile
orientationProj: cosine of the
selfCoordNum
cutoff3
selfCoordNum: coordination number between
cutoff
selfCoordNum: coordination number between
expDenom
selfCoordNum: coordination number between
expNumer
selfCoordNum: coordination number between
group1
selfCoordNum: coordination number between
group2
selfCoordNum: coordination number between
spinAngle
atoms
spinAngle: angle of rotation
refPositions
spinAngle: angle of rotation
refPositionsCol
spinAngle: angle of rotation
refPositionsColValue
spinAngle: angle of rotation
refPositionsFile
spinAngle: angle of rotation
tilt
atoms
tilt: cosine of the
axis
tilt: cosine of the
refPositions
tilt: cosine of the
refPositionsCol
tilt: cosine of the
refPositionsColValue
tilt: cosine of the
refPositionsFile
tilt: cosine of the
color
access definitions
colorinfo
assignment
Comparing Two Structures
background
Color Window
category
Color Window | Color categories | Color categories | Coloring by color categories | colorinfo | Coloring Trick - Override
command
Coloring Methods | Tcl Text Commands | axes
id
Draw Style Tab | Coloring Methods
in user-defined graphics
graphics
index
colorinfo
map
Color Window
material properties
graphics | graphics
names
Coloring Methods | colorinfo
properties
colorinfo
Python module
color
redefinition
Changing the RGB Value | Creating a set of
revert to default
Revert all RGB values
scale
Color Scale | Color scale | Color scale | color | Changing the color scale
changing
Color Scale
set minmax
mol | molrep
window
Comparing Two Structures | Color Window | Coloring Methods | Color categories | Coloring by color categories
color map
Color categories
colorinfo
command
Tcl Text Commands | colorinfo
coloring
by category
Coloring by color categories
by color scale
Color scale | Color scale
by property
Coloring Trick - Override
methods
Viewing a molecule: Myoglobin | Graphics Window | Molecular Drawing Methods | Coloring Methods | Coloring Methods | Coloring Methods | mol | mol | Coloring Trick - Override
Colvars
cv command
Using the cv command
Command line options
VMD Command-Line Options
contact residues
Finding contact residues
copyright
Copyright and Disclaimer Notices
Coulomb potential
volumetric data
volmap
cross correlation
mdffi
culling
display
debug
command
Tcl Text Commands
density
volumetric data
volmap
depth cue
display
depth cueing
Display Menu and Display
Depth of Field
Display Menu and Display
display
ambient occlusion
display
antialiasing
display
backgroundgradient
Display Menu and Display | display
command
Tcl Text Commands | colorinfo
depth of field
display
device
VMD Command-Line Options
dof
display
Python module
display
update
display | Using the molinfo command | Creating a set of | Revert all RGB values
window
Display Menu and Display
distance
volumetric data
volmap
distance between atoms
Comparing Two Structures
DoF
Display Menu and Display
draw
command
draw
drawing
method
Viewing a molecule: Myoglobin | Graphics Window
drawn
Main Window Molecule List
electrostatics
volumetric data
volmap
environment variables
Environment Variables
DISPLAY
Environment Variables
MSMSSERVER
MSMS
SURF_BIN
Surf
TCL_LIBRARY
Core Script Files
VMD_EXCL_GL_EXTENSIONS
Environment Variables
VMDBABELBIN
Babel interface | Environment Variables
VMDCAVEMEM
Environment Variables
VMDCUDADEVICEMASK
Environment Variables
VMDCUSTOMIZESTARTUP
Environment Variables
VMDDIR
Environment Variables
VMDDISABLESTEREO
Environment Variables
VMDFILECHOOSER
Environment Variables
VMDFORCECONSOLETTY
Environment Variables
VMDFORCECPUCOUNT
Environment Variables
VMDFREEVRMEM
Environment Variables
VMDGDISPLAY
Environment Variables
VMDGLSLVERBOSE
Environment Variables
VMDHTMLVIEWER
Environment Variables
VMDIMAGEVIEWER
Environment Variables
VMDIMMERSADESKFLIP
Environment Variables
VMDMACENABLEEEXTENSIONS
Environment Variables
VMDMAXAASAMPLES
Environment Variables
VMDMSECDELAYHACK
Environment Variables
VMDMSMSUSEFILE
Environment Variables
VMDNOCUDA
Environment Variables
VMDOPTIX_CLUSTER
Environment Variables
VMDOPTIX_PASSWD
Environment Variables
VMDOPTIX_USER
Environment Variables
VMDOPTIXAOMAXDIST
Environment Variables
VMDOPTIXBITRATE
Environment Variables
VMDOPTIXBUILDER
Environment Variables
VMDOPTIXDEVICE
Environment Variables
VMDOPTIXDEVICEMASK
Environment Variables
VMDOPTIXDOMEMASTER
Environment Variables
VMDOPTIXEQUIRECTANGULAR
Environment Variables
VMDOPTIXHEADLIGHT
Environment Variables
VMDOPTIXIMAGESIZE
Environment Variables
VMDOPTIXNODISPLAYGPUS
Environment Variables
VMDOPTIXSTEREO
Environment Variables
VMDOPTIXVCACONFIG"
Environment Variables
VMDOPTIXVCANODES
Environment Variables
VMDOSPRAYAOMAXDIST
Environment Variables
VMDOSPRAYIMAGESIZE
Environment Variables
VMDOSPRAYMPI
Environment Variables
VMDPREFERSTEREO
Environment Variables
VMDSCRDIST
Environment Variables
VMDSCRHEIGHT
Environment Variables
VMDSCRPOS
Environment Variables
VMDSCRSIZE
Environment Variables
VMDSHEARSTEREO
Environment Variables
VMDSIMPLEGRAPHICS
Environment Variables
VMDSPACEBALLPORT
Spaceball Driver
VMDTMPDIR
Environment Variables
VMDWIREGL
Environment Variables
evaltcl
Python module
evaltcl
example scripts
Python
calculation
atom selections
Changing the selection and
changing properties of a selection
An atom selection example
combining atom selections
Combining atom selections
loading molecules
Molecule
RMSD
RMS example
callbacks
Python callbacks
drawing
creating representations
MoleculeRep
Tcl
calculation
center of mass of a selection
Using the atomselect command
geometric center of a selection
Using the atomselect command
mass of a picked atom
Tcl callbacks
matrix transformations
Matrix routines
min and max atom coordinates
Coordinate min and max
move selected atoms
Using the atomselect command
radius of gyration
Radius of gyration
RMSD between two frames
Root mean square deviation
RMSD for all trajectory frames
A simulation example script
total mass of a selection
Total mass of a
customized startup file example
.vmdrc and vmd.rc Files
drawing
arrows
draw
changing color scales
Changing the color scale
coloring by distance
Root mean square deviation
defining grayscale colors
Creating a set of
labels
draw
rendering stereo pairs
Making Stereo Images
reverting colors to defaults
Revert all RGB values
saving and restoring the viewpoint
Using the molinfo command
exit
command
Tcl Text Commands
eye separation
Stereo Parameters | display
file
load
Viewing a molecule: Myoglobin
file types
input
Loading A Molecule | Reading Trajectory Frames
output
Saving Trajectory Frames
files
output
Rendering an Image
read
animate
reading
Viewing a molecule: Myoglobin | A Quick Animation | Loading A Molecule | Molecule File Browser Window | Reading Trajectory Frames | mol
startup
Hot Keys | VMD Command-Line Options | Startup Files | .vmdrc and vmd.rc Files
writing
Saving Trajectory Frames | animate
fit
RMSD
RMS and scripting | RMSD Computation
focal length
Stereo Parameters | display
frame
delete
Deleting Trajectory Frames | animate
duplicate
animate
write
animate
frames
Main Window Molecule List
frames per second indicator
Display Menu and Display
geometric center
Using the atomselect command
gettimestep
command
Tcl Text Commands | graphics
gopython
command
Using the Python interpreter
graphics
command
graphics
delete
graphics
loading
graphics
primitives
graphics
Python module
graphics
replace
graphics
user-defined
draw
window
Graphics Window
Gromacs
files
Loading A Molecule | Reading Trajectory Frames
gyration, radius of
Radius of gyration
hardware requirements
Hardware and Software Requirements
help
Help
command
Tcl Text Commands | gettimestep
topics
help
highlight
Selecting residues from the
hot keys
Hot Keys | user
animation control
Hot Keys
customizing
Hot Keys
menu control
Hot Keys
mouse control
Hot Keys
rotation and scaling
Hot Keys
hydrogen bonds
HBonds | measure
image
lighting controls
Mouse Modes | Display Menu and Display
shading and material properties
Material Window
imd
Interactive Molecular Dynamics
command
Tcl Text Commands | help
Python module
imd
requirements
IMD Connect Simulation Window
implicit ligand sampling
volumetric data
volmap
Interactive Molecular Dynamics
Interactive Molecular Dynamics
interpolation
volumetric data
volmap
joystick
using
Using the Joystick in
label
command
Tcl Text Commands | imd
Python module
label
labels
Comparing Two Structures
categories
Label categories | label
delete
Modifying or deleting a
hide
Modifying or deleting a
picking with mouse
Pick Modes
plotting
Plotting a label's value | Tcl callbacks
show
Modifying or deleting a
text
draw
window
Labels Window
light
command
Tcl Text Commands | label
controlling with mouse
Mouse Modes
toggle
Display Menu and Display
logfile
command
Tcl Text Commands | logfile
disable from GUI
Tracking Script Command Versions
disable from text
logfile
enable from GUI
Tracking Script Command Versions
enable from text
logfile
logging tcl commands
Tracking Script Command Versions | logfile
mask
volumetric data
volmap
mass
center of
Using the atomselect command
of residue atoms
Tcl callbacks
total
Total mass of a
material
changing
mol | mol
command
Tcl Text Commands | logfile
methods
Graphics Window
Python module
material
material properties
graphics | graphics
matrix routines
alignment
Matrix routines
identity
Matrix routines
inverse alignment
Matrix routines
list of
Matrix routines
multiplication
Matrix routines
rotation
Matrix routines
trans command
Matrix routines
translation
Matrix routines
transpose
Matrix routines
MDFF
mdffi
mdffi
command
Tcl Text Commands | mdffi
MDTools
For information on our
measure
command
Tcl Text Commands | measure | Analysis scripts | Coordinate min and max
menu
command
Tcl Text Commands | measure
menus
menu
molecular surface
QuickSurf | Surf | MSMS
molecule
active
Main Window Molecule List | Main Window Animation Controls
analysis
Analysis scripts
best-fit alignment
Computing the Alignment
command
Tcl Text Commands | menu | mol
data
molinfo
deleting
Deleting a Molecule
drawn
Main Window Molecule List
fixed
Comparing Two Structures | Main Window Molecule List
graphics
graphics
id
mol
index
mol
info
Molecular Analysis
list
Main Window Molecule List
loading
Viewing a molecule: Myoglobin | A Quick Animation | graphics | Root mean square deviation
Python module
molecule
status
Main Window Molecule List | mol
changing
Changing the Molecule's Status | mol | Using the molinfo command
top
Main Window Molecule List | Jumping to Specific Frames | molinfo
translation
Comparing Two Structures
molinfo
command
molecule | Molecular Analysis
keywords
molinfo
molrep
Python module
molrep
mouse
add or remove bonds
Mouse Modes
callback
mouse
command
Tcl Text Commands | molinfo
modes
Viewing a molecule: Myoglobin | Comparing Two Structures | Mouse Modes | Hot Keys | mouse
mouse mode
Mouse modes
move
Pick modes
atom
Pick modes
fragment
Pick modes
highlighted rep
Pick modes
molecule
Pick modes
residue
Pick modes
object menus
Pick modes
pick information
Pick information
rocking
mouse
stop rotation
mouse
using
Using the Mouse in
movies
Making a Movie
NAMD
For information on our
files
Loading A Molecule | Reading Trajectory Frames
occupancy
volumetric data
volmap
orthographic view
Display Menu and Display | Perspective/Orthographic views
output
format
Rendering an Image
parallel
command
Tcl Text Commands | mouse
PCRE
Copyright and Disclaimer Notices
periodic boundary conditions
Periodic Tab
periodic image display
Periodic Tab
perspective view
Display Menu and Display | Perspective/Orthographic views
picking
angles
Pick Modes | Pick Modes
atoms
Comparing Two Structures | Pick Modes | Pick Modes
bonds
Comparing Two Structures | Pick Modes | Pick Modes
center
Pick Modes
dihedrals
Pick Modes | Pick Modes
distances
Comparing Two Structures
hot keys
Hot Keys
modes
Comparing Two Structures | Pick Modes
move atom
Pick Modes
move fragment
Pick Modes
move highlighted rep
Pick Modes
move molecule
Pick Modes
move residue
Pick Modes
query
Pick Modes
text command
mouse
play
command
Using text commands | Tcl Text Commands | parallel | VMD Command-Line Options
plot
geometry monitors
Plotting a label's value
postscript
One Step Printing
potential of mean force
volumetric data
volmap
Python
Copyright and Disclaimer Notices
atomsel
The built-in atomsel type
environment variables
Python modules within VMD
interface
Python Text Interface
libraries
Python modules within VMD
Numeric
Python modules within VMD | vmdnumpy
RMSD
The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED)
startup
VMD Command-Line Options
Tkinter
Python modules within VMD | Using Tkinter menus in
version
Python Text Interface
quit
Main Window
command
draw | play
quoting
Quoting with Single Quotes
radius of gyration
Radius of gyration
Ramachandran plot
RamaPlot
Raster3D
Raster3D file format | Making Stereo Images
regular expression
Double Quotes and Regular | Double Quotes and Regular
X-PLOR conversion
Double Quotes and Regular
remote
connection
imd
detaching
IMD Using the Simulation
killing
IMD Using the Simulation
modifiable parameters
IMD Using the Simulation
options
imd
simulation control
imd
render
command
Tcl Text Commands | quit
Python module
render
window
Rendering an Image | Render Window
rendering
Rendering an Image | Render Window | Scene Export and Rendering
ambient occlusion lighting
display | render
antialiasing
render
ART
Higher Quality Rendering
caveats and considerations
Caveats
exec command
render
Gelato
Higher Quality Rendering
in background process
Render Window
list of supported renderers
Higher Quality Rendering
methods
Higher Quality Rendering | render
PostScript
Higher Quality Rendering
POV-Ray
Higher Quality Rendering
Radiance
Higher Quality Rendering
Raster3D
Higher Quality Rendering
Rayshade
Higher Quality Rendering
RenderMan
Higher Quality Rendering
stereo
Making Stereo Images
STL
Higher Quality Rendering
Tachyon
Acknowledgments | Copyright and Disclaimer Notices | Rendering an Image | Higher Quality Rendering | render
TachyonInternal
Higher Quality Rendering | render
TachyonLOptiXInteractive
Higher Quality Rendering
TachyonLOptiXInternal
Higher Quality Rendering
TachyonLOSPRayInteractive
Higher Quality Rendering
TachyonLOSPRayInternal
Higher Quality Rendering
VRML-1
Higher Quality Rendering
VRML-2
Higher Quality Rendering
Wavefront
Higher Quality Rendering
X3D
Higher Quality Rendering
X3DOM
Higher Quality Rendering
rendering modes
display
rendermode
Display Menu and Display
representation
Molecular Drawing Methods | mol
add new
Adding a rep.
adding
Adding a rep.
auto-update
Selection and Color auto-update.
Beads
Beads
Bonds
Bonds
Cartoon
Cartoon
changing
An Introduction to Atom | Changing a rep. | mol
clipping planes
user defined
mol
CPK
CPK
deleting
Deleting a rep. | Deleting a rep.
dotted van der Waals
Dotted
draw multiple frames
mol
DynamicBonds
DynamicBonds
examples
Some Nice Represenations
FieldLines
FieldLines
HBonds
HBonds
hiding
Hiding a rep.
Isosurface
Isosurface
Licorice
Licorice
Lines
Lines
list of available
Rendering methods
MSMS
MSMS
NewCartoon
NewCartoon
NewRibbons
NewRibbons
Orbital
Orbital
PaperChain
PaperChain
Points
Points
Polyhedra
Polyhedra
QuickSurf
QuickSurf
Ribbons
Ribbons
show/hide
mol | molrep
solvent representation
Solvent
style
Viewing a molecule: Myoglobin | Graphics Window | Molecular Drawing Methods | mol
Surf
Surf
Trace
Trace
Tube
Tube
Twister
Twister
van der Waals
VDW
VolumeSlice
VolumeSlice
represention
auto-update
mol
reset view
Display Menu and Display
resetview
display
restore
viewpoint
Using the molinfo command
vmd state
Saving your work
RMS
Fit
RMS Fit and Alignment
RMS:Alignment
RMS Fit and Alignment
RMSD
The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | The AtomSel class (DEPRECATED) | RMS example | Root mean square deviation | RMS and scripting | RMSD Computation | A simulation example script
rock
Looping Styles
command
Tcl Text Commands | render
rotate
command
Tcl Text Commands | rock
side chain
Using the atomselect command
rotation
continuous
Mouse Modes
hot keys
Hot Keys
stop
Mouse Modes
using mouse
Mouse Modes
save
configuration
Saving your work
logfile
Tracking Script Command Versions
viewpoint
Using the molinfo command
vmd state
Saving your work | Saving and Restoring Molecule
scale
command
Tcl Text Commands | rotate
scaling
using mouse
Mouse Modes
screen parameters
Display Menu and Display
scripts
play
Using text commands
source
Using text commands
secondary structure codes
Sequence information
selection
Viewing a molecule: Myoglobin | An Introduction to Atom | Graphics Window | Molecular Drawing Methods | atomselect | mol | Using the atomselect command
comparison
Comparison selections
keywords
Selections Tab | Selection Methods | Definition of Keywords and
boolean
Boolean Keywords
logic
Short Circuiting
math functions
Definition of Keywords and
modes
Selection Methods
text
Using the atomselect command
volumetric data
Definition of Keywords and
sensor configuration file
Configuring input devices
sensors
Configuring input devices
sequence
Sequence information
caveats
Caveats
dna
Sequence Window
window
Sequence Window
zooming
Sequence Zooming
Shadows
Display Menu and Display
short circuit logic
Short Circuiting | within and same
sleep
command
Tcl Text Commands | wait
source
command
Using text commands
spaceball
driver
Acknowledgments | Spaceball Driver
serial
Spaceball Driver
windowing system
Spaceball Driver
modes
Using the Spaceball in
using
Using the Spaceball in
SpaceNavigator
driver
Spaceball Driver
windowing system
Spaceball Driver
modes
Using the Spaceball in
using
Using the Spaceball in
stage
Display Menu and Display
command
Tcl Text Commands | scale
startup files
Hot Keys | VMD Command-Line Options | Startup Files | .vmdrc and vmd.rc Files
stereo
mode
Stereoscopic Modes
checkerboard
Checkerboard Stereo
column interleaved
Column Interleaved Stereo
cross-eyed
Side-By-Side and Cross-Eyed Stereo
CrystalEyes
Quad-buffered Stereo
HDTV side-by-side
HDTV Side-by-side Stereo
quad buffered
Quad-buffered Stereo
row interleaved
Row Interleaved Stereo
scanline interleaved
Row Interleaved Stereo | Anaglyph Stereo
side-by-side
Side-By-Side and Cross-Eyed Stereo
off
Monoscopic Modes
parameters
Display Menu and Display | Stereo Parameters | display | display
STL files
Higher Quality Rendering
stop rotation
Display Menu and Display
stride
Copyright and Disclaimer Notices
surf
Copyright and Disclaimer Notices
surface
molecular
Solvent
solvent accessible
Solvent
Tachyon
Copyright and Disclaimer Notices
TachyonInternal
Making Stereo Images
Tcl
Tcl/Tk
tcl commands
Tcl Text Commands
text
displayed
graphics
Tk
Tcl/Tk
tool
CAVE
Configuring input devices
command
Tcl Text Commands | stage
FreeVR
Configuring input devices
Spaceball
Configuring input devices
VRPN
Configuring input devices
window
Tool Window
tools
Using Tools
topology files
Loading A Molecule
trajectory
draw multiple frames
Draw Multiple Frames. | mol
files
Loading A Molecule
read
Reading Trajectory Frames
smoothing
Trajectory Smoothing. | mol | molrep
write
Saving Trajectory Frames
trans
Python module
trans
translate
command
Tcl Text Commands | tool
translation
change atom coordinates
Using the atomselect command
using mouse
Mouse Modes
transparency
Draw Style Tab
unit cell information
Periodic Tab
universal sensor locator
Configuring input devices
user
command
Tcl Text Commands | translate
user interfaces
python
Python Text Interface
text
Tcl Text Interface
USL
Configuring input devices
variables
env
Environment Variables | Core Script Files
M_PI
Misc. functions and values
trace
Tcl callbacks
vector command
coordtrans
Multiplying vectors and matrices
vecadd
Vectors | Vectors
veccross
Vectors
vecdist
Vectors
vecdot
Vectors
vecinvert
Vectors
veclength
Vectors
veclength2
Vectors
vecmean
Vectors
vecnorm
Vectors
vecscale
Vectors
vecstddev
Vectors
vecsub
Vectors
vecsum
Vectors
vectrans
Multiplying vectors and matrices
veczero
Vectors
vector routines
Vectors and Matrices
view
mol
viewing modes
changing
Viewing Modes
VMD
as MIME helper application
MIME types
command line options
VMD Command-Line Options
compile options
vmdinfo
copyright
Copyright and Disclaimer Notices
customizing
Hot Keys | Customizing VMD Sessions
vmdinfo
command
Tcl Text Commands | user
volmap
command
Tcl Text Commands | volmap
volumetric data
VolumeSlice | Isosurface
generating
volmap
VRML files
Higher Quality Rendering
wait
command
Tcl Text Commands | Implicit Ligand Sampling (volmap
window
animate
A Quick Animation
color
Comparing Two Structures | Color Window | Coloring Methods | Color categories | Coloring by color categories
display
Display Menu and Display
files
Viewing a molecule: Myoglobin
graphics
Viewing a molecule: Myoglobin | An Introduction to Atom | Graphics Window
hot keys
Hot Keys
IMD simulation
IMD Connect Simulation Window
label
Labels Window
main
Main Window | GUI Shortcuts
material
Material Window
molecule file browser
Molecule File Browser Window
mouse menu
Mouse Menu
RamaPlot
RamaPlot
render
Rendering an Image | Render Window
sequence
Sequence Window
tool
Tool Window
windows
menu
X3D files
Higher Quality Rendering
XPLOR
files
Loading A Molecule | Reading Trajectory Frames



vmd@ks.uiuc.edu