PLUMED-NEST

Project ID: plumID:20.004
Source: ala2/3_enhanced_sampling/plumed.dat
Originally used with PLUMED version: 2.5-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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

#DEFINE INPUTS: DISTANCES
d1:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,5
The DISTANCE action with label d1 calculates a scalar quantityd2:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,6
The DISTANCE action with label d2 calculates a scalar quantityd3:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,7
The DISTANCE action with label d3 calculates a scalar quantityd4:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,9
The DISTANCE action with label d4 calculates a scalar quantityd5:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,11
The DISTANCE action with label d5 calculates a scalar quantityd6:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,15
The DISTANCE action with label d6 calculates a scalar quantityd7:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,16
The DISTANCE action with label d7 calculates a scalar quantityd8:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,17
The DISTANCE action with label d8 calculates a scalar quantityd9:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=2,19
The DISTANCE action with label d9 calculates a scalar quantityd10:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,6
The DISTANCE action with label d10 calculates a scalar quantityd11:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,7
The DISTANCE action with label d11 calculates a scalar quantityd12:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,9
The DISTANCE action with label d12 calculates a scalar quantityd13:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,11
The DISTANCE action with label d13 calculates a scalar quantityd14:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,15
The DISTANCE action with label d14 calculates a scalar quantityd15:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,16
The DISTANCE action with label d15 calculates a scalar quantityd16:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,17
The DISTANCE action with label d16 calculates a scalar quantityd17:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,19
The DISTANCE action with label d17 calculates a scalar quantityd18:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,7
The DISTANCE action with label d18 calculates a scalar quantityd19:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,9
The DISTANCE action with label d19 calculates a scalar quantityd20:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,11
The DISTANCE action with label d20 calculates a scalar quantityd21:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,15
The DISTANCE action with label d21 calculates a scalar quantityd22:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,16
The DISTANCE action with label d22 calculates a scalar quantityd23:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,17
The DISTANCE action with label d23 calculates a scalar quantityd24:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=6,19
The DISTANCE action with label d24 calculates a scalar quantityd25:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,9
The DISTANCE action with label d25 calculates a scalar quantityd26:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,11
The DISTANCE action with label d26 calculates a scalar quantityd27:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,15
The DISTANCE action with label d27 calculates a scalar quantityd28:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,16
The DISTANCE action with label d28 calculates a scalar quantityd29:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,17
The DISTANCE action with label d29 calculates a scalar quantityd30:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=7,19
The DISTANCE action with label d30 calculates a scalar quantityd31:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,11
The DISTANCE action with label d31 calculates a scalar quantityd32:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,15
The DISTANCE action with label d32 calculates a scalar quantityd33:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,16
The DISTANCE action with label d33 calculates a scalar quantityd34:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,17
The DISTANCE action with label d34 calculates a scalar quantityd35:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=9,19
The DISTANCE action with label d35 calculates a scalar quantityd36:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,15
The DISTANCE action with label d36 calculates a scalar quantityd37:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,16
The DISTANCE action with label d37 calculates a scalar quantityd38:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,17
The DISTANCE action with label d38 calculates a scalar quantityd39:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=11,19
The DISTANCE action with label d39 calculates a scalar quantityd40:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,16
The DISTANCE action with label d40 calculates a scalar quantityd41:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,17
The DISTANCE action with label d41 calculates a scalar quantityd42:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=15,19
The DISTANCE action with label d42 calculates a scalar quantityd43:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=16,17
The DISTANCE action with label d43 calculates a scalar quantityd44:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=16,19
The DISTANCE action with label d44 calculates a scalar quantityd45:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=17,19

#LOAD PYTORCH MODEL
The DISTANCE action with label d45 calculates a scalar quantitydeep: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=../2_training_model/model.pt 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45

#DEFINE OPES CALCULATION
The PYTORCH_MODEL action with label deep calculates the following quantities:
 Quantity   
 Description  
deep.node
Model outputs
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=opes
  
ARG
the input for this action is the scalar output from one or more other actions
=deep.node-0
  
PACE
the frequency for kernel deposition
=500
  
SIGMA
 the initial widths of the kernels
=0.025
  
BARRIER
the free energy barrier to be overcome
=30
... OPES_METAD

#MONITOR DIHEDRAL ANGLES
The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the biasphi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15	
The TORSION action with label phi calculates a scalar quantitypsi: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17	

#PRINT
The TORSION action with label psi calculates a scalar quantity
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
ARG
the input for this action is the scalar output from one or more other actions
=deep.node-0,phi,psi,opes 
FILE
the name of the file on which to output these quantities
=COLVAR

ENDPLUMED
Terminate plumed input. More details


#alternative: WT-METAD CALCULATION
METAD ...
LABEL=meta
ARG=deep.node-0 
PACE=500 
HEIGHT=1.25 
SIGMA=0.025 
BIASFACTOR=6.00
TEMP=300.0
GRID_MIN=-2
GRID_MAX=2
GRID_BIN=750
CALC_RCT
... METAD