Project ID: plumID:19.056
Source: 4w54/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
UNITSThis command sets the internal units for the code. More detailsLENGTH=Athe units of lengthsTIME=psthe units of timeENERGY=kcal/molthe units of energyMAZE_LOSS...Define a coarse-grained loss function describing interactions in a More detailsLABEL=la label for the action so that its output can be referenced in the input to other actionsPARAMS=1,1,1 ... MAZE_LOSSParameters for the loss functionMAZE_SIMULATED_ANNEALING...Calculates the biasing direction along which the ligand unbinds by minimizing More detailsLABEL=opta label for the action so that its output can be referenced in the input to other actionsLOSS=lLoss function describing ligand-protein interactions required by every optimizerN_ITER=1000Number of optimization stepsOPTIMIZER_STRIDE=250000 # 1 nsOptimizer stridePROBABILITY_DECREASER=300Temperature-like parameter that is decreased during optimization to modify the Metropolis-Hastings acceptance probabilityCOOLING=0.95Reduction factor for PROBABILITY_DECREASER, should be in (0, 1]COOLING_SCHEME=geometricCooling scheme: geometricLIGAND=2635-2649Indices of ligand atomsPROTEIN=1-2634Indices of protein atomsNLISTUse a neighbor list of ligand-protein atom pairs to speed up the calculating of the distancesNL_CUTOFF=7Neighbor list cut-off for the distances of ligand-protein atom pairsNL_STRIDE=100 ... MAZE_SIMULATED_ANNEALINGUpdate stride for the ligand-protein atom pairs in the neighbor list
p:POSITIONCalculate the components of the position of an atom. More detailsATOM=2640the atom numberNOPBCignore the periodic boundary conditions when calculating distancesMAZE_OPTIMIZER_BIAS...Biases the ligand along the direction calculated by the chosen ef MAZE_OPTIMIZER. More detailsLABEL=ba label for the action so that its output can be referenced in the input to other actionsARG=p.x,p.y,p.zthe input for this action is the scalar output from one or more other actionsBIASING_RATE=0.03Biasing rateALPHA=3.6Rescaled force constantOPTIMIZER=opt ... MAZE_OPTIMIZER_BIASOptimization technique to minimize the collective variable for ligand unbinding: RANDOM_WALK, STEERED_MD, RANDOM_ACCELERATION_MD, SIMULATED_ANNEALING, MEMETIC_SAMPLINGPrint quantities to a file. More detailsARG=opt.loss,opt.sr,b.bias,b.force2,b.tdistthe input for this action is the scalar output from one or more other actionsSTRIDE=500the frequency with which the quantities of interest should be outputFILE=colvarthe name of the file on which to output these quantitiesFMT=%15.8f ... PRINTthe format that should be used to output real numbers