PLUMED-NEST-TEST-SITE

Project ID: plumID:19.066
Source: 4w52/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps ENERGYthe units of energy=kcal/mol

The UNITS action with label  calculates somethingMAZE_LOSSDefine a coarse-grained loss function describing interactions in a More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=l

  PARAMSParameters for the loss function=1,1,1
... MAZE_LOSS

The MAZE_LOSS action with label l calculates the following quantities:
 Quantity   
 Description  
l.value
the value of the loss functionMAZE_SIMULATED_ANNEALINGCalculates the biasing direction along which the ligand unbinds by minimizing More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=optThe MAZE_SIMULATED_ANNEALING action with label opt calculates the following quantities:
 Quantity   
 Type   
 Description  
opt.x
scalar
Optimal biasing direction; x component.
opt.y
scalar
Optimal biasing direction; y component.
opt.z
scalar
Optimal biasing direction; z component.
opt.loss
scalar
Loss function value defined by the provided pairing function.
opt.sr
scalar
Sampling radius. Reduces sampling to the local proximity of the ligand position.
  
  LOSSLoss function describing ligand-protein interactions required by every optimizer=l
  
  N_ITERNumber of optimization steps=1000
  OPTIMIZER_STRIDEOptimizer stride=50000

  PROBABILITY_DECREASERTemperature-like parameter that is decreased during optimization to modify the Metropolis-Hastings acceptance probability=300
  COOLINGReduction factor for PROBABILITY_DECREASER, should be in (0, 1]=0.95
  COOLING_SCHEMECooling scheme: geometric=geometric  
   
  LIGANDIndices of ligand atoms=2635-2646
  PROTEINIndices of protein atoms=1-2634

  NLIST Use a neighbor list of ligand-protein atom pairs to speed up the calculating of the distances
  NL_CUTOFFNeighbor list cut-off for the distances of ligand-protein atom pairs=7
  NL_STRIDEUpdate stride for the ligand-protein atom pairs in the neighbor list=100
... MAZE_SIMULATED_ANNEALING

pThe POSITION action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.x
scalar
the x-component of the atom position
p.y
scalar
the y-component of the atom position
p.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=2640 NOPBC ignore the periodic boundary conditions when calculating distances

MAZE_OPTIMIZER_BIASBiases the ligand along the direction calculated by the chosen MAZE_OPTIMIZER. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=bThe MAZE_OPTIMIZER_BIAS action with label b calculates the following quantities:
 Quantity   
 Type   
 Description  
b.bias
scalar
the instantaneous value of the bias potential
b.force2
scalar
Square of the biasing force.
b.x
scalar
Optimal biasing direction: x component.
b.y
scalar
Optimal biasing direction: y component.
b.z
scalar
Optimal biasing direction: z component.
b.tdist
scalar
Total distance traveled by biased atoms.  

  ARGthe labels of the scalars on which the bias will act=p.x,p.y,p.z

  BIASING_RATEBiasing rate=0.02
  ALPHARescaled force constant=3.6
  OPTIMIZEROptimization technique to minimize the collective variable for ligand     unbinding: RANDOM_WALK,                STEERED_MD,                RANDOM_ACCELERATION_MD,                SIMULATED_ANNEALING,                MEMETIC_SAMPLING=opt
... MAZE_OPTIMIZER_BIAS

PRINTPrint quantities to a file. More details ...
  ARGthe labels of the values that you would like to print to the file=opt.loss,opt.sr,b.bias,b.force2,b.tdist
  STRIDE the frequency with which the quantities of interest should be output=500
  FILEthe name of the file on which to output these quantities=colvar
  FMTthe format that should be used to output real numbers=%15.8f 
... PRINT