Project ID: plumID:19.056
Source: 4w56/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
tested onv2.9
tested onmaster
UNITS
This command sets the internal units for the code. More details
LENGTH
the units of lengths
=A
TIME
the units of time
=ps
ENERGY
the units of energy
=kcal/mol
MAZE_LOSS
Define a coarse-grained loss function describing interactions in a More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=l
PARAMS
Parameters for the loss function
=1,1,1 ... MAZE_LOSS
MAZE_SIMULATED_ANNEALING
Calculates the biasing direction along which the ligand unbinds by minimizing More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opt
LOSS
Loss function describing ligand-protein interactions required by every optimizer
=l
N_ITER
Number of optimization steps
=1000
OPTIMIZER_STRIDE
Optimizer stride
=250000 # 1 ns
PROBABILITY_DECREASER
Temperature-like parameter that is decreased during optimization to modify the Metropolis-Hastings acceptance probability
=300
COOLING
Reduction factor for PROBABILITY_DECREASER, should be in (0, 1]
=0.95
COOLING_SCHEME
Cooling scheme: geometric
=geometric
LIGAND
Indices of ligand atoms
=2635-2658
PROTEIN
Indices of protein atoms
=1-2634
NLIST
Use a neighbor list of ligand-protein atom pairs to speed up the calculating of the distances
NL_CUTOFF
Neighbor list cut-off for the distances of ligand-protein atom pairs
=7
NL_STRIDE
Update stride for the ligand-protein atom pairs in the neighbor list
=100 ... MAZE_SIMULATED_ANNEALING
p:
POSITION
Calculate the components of the position of an atom. More details
ATOM
the atom number
=2640
NOPBC
ignore the periodic boundary conditions when calculating distances

MAZE_OPTIMIZER_BIAS
Biases the ligand along the direction calculated by the chosen ef MAZE_OPTIMIZER. More details
...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=b
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y,p.z
BIASING_RATE
Biasing rate
=0.03
ALPHA
Rescaled force constant
=3.6
OPTIMIZER
Optimization technique to minimize the collective variable for ligand unbinding: RANDOM_WALK, STEERED_MD, RANDOM_ACCELERATION_MD, SIMULATED_ANNEALING, MEMETIC_SAMPLING
=opt ... MAZE_OPTIMIZER_BIAS
PRINT
Print quantities to a file. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=opt.loss,opt.sr,b.bias,b.force2,b.tdist
STRIDE
the frequency with which the quantities of interest should be output
=500
FILE
the name of the file on which to output these quantities
=colvar
FMT
the format that should be used to output real numbers
=%15.8f ... PRINT