About VLMP
What is VLMP?
Installation
First example
Design and Usage
Components
Simulation
Order
Simulation Pool
VLMP Execution
Local Execution
HPC Cluster
Workflow
Experiments
Components
Systems
backup
seed
simulationName
Units
KcalMol_A
none
Types
basic
none
Ensembles
NVT
NVTlambda
Models
CORONAVIRUS
ENM
FILE
HELIX
ICOSPHERE
IDP
KB
MADna
MAGNETICNP
MEMBRANE
PARTICLE
PROTEIN_IDP_PROTEIN
SBCG
SIMULATION
SOP
SPHEREMULTIBLOB
STERIC_LAMBDA_SOLVATION
WLC
ModelOperations
alignInertiaMomentAlongVector
distributeRandomly
rotation
setCenterOfMassPosition
setContactDistance
setParticleLowestPosition
setParticlePositions
setParticleXYPosition
ModelExtensions
ACMagneticField
AFM
LennardJones
WCA
absortionSurface
addBond
constantForce
constantForceBetweenCentersOfMass
constantForceOverCenterOfMass
constantTorqueBetweenCentersOfMass
constantTorqueOverCenterOfMass
constraintCenterOfMassPosition
constraintParticlesListPositionLambda
constraintParticlesPosition
constraintParticlesPositionLambda
harmonicBondBetweenCentersOfMass
helixBoundaries
plates
sphericalShell
steric
surface
surfaceMaxForce
uniformMagneticField
Integrators
BBK
EulerMaruyama
EulerMaruyamaRigidBody
EulerMaruyamaRigidBodyPatchesState
GFJ
MagneticBrownian
NVE
SimulationSteps
AFMMaxForce
afmMeasurement
anglesMeasurement
centerOfMassMeasurement
forceBetweenSetsMeasurement
gyrationRadius
heightMeasurement
info
lambdaActivation
lambdaCycle
meanMagnetizationMeasurement
meanRadius
meanSquareDisplacement
nativeContactsMeasurement
oscillatoryForceMeasurement
pairwiseForces
patchPolymersMeasurement
potentialEnergyMeasurement
potentialMeasurement
savePatchyParticlesState
saveState
stressMeasurement
thermodynamicIntegration
thermodynamicMeasurement
vqcmMeasurement
vqcmMeasurementFromMobility
Experiments
HighThroughputAFM
Introduction
Setting Up the Experiment
Running the Simulations
Analyzing the Results
Customizing Your Experiment
Advanced Usage
Conclusion
SurfaceUmbrellaSampling
Introduction
Setting Up the Experiment
Running the Simulations
Analyzing the Results
Customizing Your Experiment
Conclusion
References
Extending VLMP
How to Extend VLMP
Install Extension
Sharing Your Extension
Templates
SYSTEM
UNITS
TYPES
ENSEMBLE
MODELS
MODEL_OPERATIONS
MODEL_EXTENSIONS
INTEGRATORS
SIMULATION_STEPS
VLMP
»
Index
Index