PLUMED-NEST

Project ID: plumID:23.017
Source: classical_biased_MD/plumed.dat
Originally used with PLUMED version: 2.9
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

# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---

protein: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-7654
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=protein
FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
STRIDE
 the frequency with which molecules are reassembled
=1 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=npt_eqm3_align2z_CA.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL


##################################################################################################
# --- (2) CONTACT DESCRIPTORS ---

#....Reactive Criteria 1............
Dnu1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3026 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7699 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.55 NN=6 MM=10}
The COORDINATION action with label Dnu1 calculates a scalar quantityDnu2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3027 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7699 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.55 NN=6 MM=10}

The COORDINATION action with label Dnu2 calculates a scalar quantityNu1-CH2OH: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3026 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7716 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.35 NN=6 MM=10}
The COORDINATION action with label Nu1-CH2OH calculates a scalar quantityNu2-CH2OH: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3027 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7716 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.35 NN=6 MM=10}

The COORDINATION action with label Nu2-CH2OH calculates a scalar quantityNu1-acid: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3026 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=3606 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.35 NN=6 MM=10}
The COORDINATION action with label Nu1-acid calculates a scalar quantityNu2-acid: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3027 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=3606 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.35 NN=6 MM=10}

#....Reactive Criteria 2............
The COORDINATION action with label Nu2-acid calculates a scalar quantityDacid: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=3607 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7698 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.45 NN=6 MM=10}

#....Reactive Criteria 3............
The COORDINATION action with label Dacid calculates a scalar quantitystrHbond-O21: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4654 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7703 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10}
The COORDINATION action with label strHbond-O21 calculates a scalar quantitystrHbond-O22: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4655 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7703 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10}

The COORDINATION action with label strHbond-O22 calculates a scalar quantitystrHbond-O31: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4654 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7707 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10}
The COORDINATION action with label strHbond-O31 calculates a scalar quantitystrHbond-O32: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=4655 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=7707 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10}

The COORDINATION action with label strHbond-O32 calculates a scalar quantityD300_torsion: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=4646,4648,4650,4653 #N-CA-CB-CG torsion of residue 300
The TORSION action with label D300_torsion calculates a scalar quantitycos_torsion: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=D300_torsion 
FUNC
the function you wish to evaluate
=cos(x 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-1,1

# --- Z-distance DESCRIPTOR ---
D197CA: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=3020
lig: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=7678-7719  #The reactive rings of the ligand (residue 500 and 501)
D_nu-lig: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=D197CA,lig 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label


##################################################################################################
# --- (3) WATER DESCRIPTORS ---

The DISTANCE action with label D_nu-lig calculates the following quantities:
 Quantity   
 Description  
D_nu-lig.x
the x-component of the vector connecting the two atoms
D_nu-lig.y
the y-component of the vector connecting the two atoms
D_nu-lig.z
the z-component of the vector connecting the two atomsWO: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=7765-67992:3  #water molecules

ligO4: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=7698   #Solvation of ligand (resid 500)
ligO2: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=7703   #Solvation of ligand (resid 501)
ligO3: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=7707   #Solvation of ligand (resid 501)
ligO6: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=7716   #Solvation of ligand (resid 501)

D197: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=3025   #Bindong pose selected atom
D300: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=4653   #Bindong pose selected atom

# Hydration spots
 v1:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=4.4475,4.6727,5.4427
 v2:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=4.5887,4.7353,5.3047
 v3:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=4.7473,4.5323,5.2327
 v4:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=4.7796,4.6265,5.1469
 v5:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=4.9981,4.6302,5.2047
 v6:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=5.1255,4.7229,5.2486
 v7:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=5.0725,4.8750,5.2862
 v8:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=4.8496,4.9004,5.2126
 v9:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=5.0243,5.0961,5.3479
v10:    
FIXEDATOM
Add a virtual atom in a fixed position. More details
 
AT
coordinates of the virtual atom
=5.0874,5.2668,5.3580


# --- DESCRIPTORS ---
NligO2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=ligO2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label NligO2 calculates a scalar quantityNligO3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=ligO3 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label NligO3 calculates a scalar quantityNligO4: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=ligO4 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label NligO4 calculates a scalar quantityNligO6: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=ligO6 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20

The COORDINATION action with label NligO6 calculates a scalar quantityND197: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=D197 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.35 NN=6 MM=10 D_MAX=0.8} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label ND197 calculates a scalar quantityND300: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=D300 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.35 NN=6 MM=10 D_MAX=0.8} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20

The COORDINATION action with label ND300 calculates a scalar quantitycvwo1:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v1  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo1 calculates a scalar quantitycvwo2:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v2  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo2 calculates a scalar quantitycvwo3:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v3  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo3 calculates a scalar quantitycvwo4:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v4  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo4 calculates a scalar quantitycvwo5:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v5  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo5 calculates a scalar quantitycvwo6:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v6  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo6 calculates a scalar quantitycvwo7:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v7  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo7 calculates a scalar quantitycvwo8:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v8  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo8 calculates a scalar quantitycvwo9:  
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v9  
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20
The COORDINATION action with label cvwo9 calculates a scalar quantitycvwo10: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=v10 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=WO 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=0.6} 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=2.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=20


# ---(4) Wall on distance to prevent exit of ligand 
The COORDINATION action with label cvwo10 calculates a scalar quantity
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=0.65 
ARG
the arguments on which the bias is acting
=D_nu-lig.z 
KAPPA
the force constant for the wall
=10000.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lower_wall_z
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=1.00 
ARG
the arguments on which the bias is acting
=D_nu-lig.z 
KAPPA
the force constant for the wall
=10000.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=upper_wall_z


##################################################################################################
# --- (5) Two deepTDA CVs ---

s_contact: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=contactCV_model.ptc 
ARG
the input for this action is the scalar output from one or more other actions
=Dnu1,Dnu2,Nu1-CH2OH,Nu2-CH2OH,Nu1-acid,Nu2-acid,strHbond-O21,strHbond-O22,strHbond-O31,strHbond-O32,Dacid,cos_torsion,D_nu-lig.z

The PYTORCH_MODEL action with label s_contact calculates the following quantities:
 Quantity   
 Description  
s_contact.node
Model outputs
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=15.0  
ARG
the arguments on which the bias is acting
=s_contact.node-0 
KAPPA
the force constant for the wall
=5000.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=upper_wall_s_contact
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=-15.0 
ARG
the arguments on which the bias is acting
=s_contact.node-0 
KAPPA
the force constant for the wall
=5000.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lower_wall_s_contact

#............................................................................................
s_water: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=water_model.ptc 
ARG
the input for this action is the scalar output from one or more other actions
=cvwo1,cvwo2,cvwo3,cvwo4,cvwo5,cvwo6,cvwo7,cvwo8,cvwo9,cvwo10,NligO2,NligO3,NligO4,NligO6,ND197,ND300

The PYTORCH_MODEL action with label s_water calculates the following quantities:
 Quantity   
 Description  
s_water.node
Model outputs
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=15.0  
ARG
the arguments on which the bias is acting
=s_water.node-0 
KAPPA
the force constant for the wall
=5000.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=upper_wall_s_water
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=-15.0 
ARG
the arguments on which the bias is acting
=s_water.node-0 
KAPPA
the force constant for the wall
=5000.0 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=lower_wall_s_water


#.....normalized deepCV................................................................
n_s_contact: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=s_contact.node-0 
FUNC
the function you wish to evaluate
=(x+14.0)/28.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
n_s_water: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=s_water.node-0 
FUNC
the function you wish to evaluate
=(x+14.0)/28.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO


#.....pathCV................................................................
pth: 
PATH
Path collective variables with a more flexible framework for the distance metric being used. More details
 
REFERENCE
a pdb file containing the set of reference configurations
=final_path.pdb 
TYPE
 the manner in which distances are calculated
=EUCLIDEAN 
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=200.0
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
AT
the positions of the wall
=0.01 
ARG
the arguments on which the bias is acting
=pth.zpath 
KAPPA
the force constant for the wall
=500000 
EXP
 the powers for the walls
=2 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=upper_pthz



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# --- (6) OPES  ---

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
=pth.spath
  
FILE
 a file in which the list of all deposited kernels is stored
=../Kernels.data
  
STATE_RFILE
read from this file the compressed kernels and all the info needed to RESTART the simulation
=../compressed.Kernels
  
STATE_WFILE
write to this file the compressed kernels and all the info needed to RESTART the simulation
=../compressed.Kernels
  
PACE
the frequency for kernel deposition
=500
  
BARRIER
the free energy barrier to be overcome
=55
  
TEMP
 temperature
=300.0
#  RESTART=YES
  
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=5000
  
WALKERS_MPI
 switch on MPI version of multiple walkers
... OPES_METAD


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 bias
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
ARG
the input for this action is the scalar output from one or more other actions
=s_contact.node-0,s_water.node-0,n_s_contact,n_s_water,pth.spath,pth.zpath,*.bias,opes.rct,opes.zed,opes.neff,opes.nker 
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%8.4f