PLUMED-NEST

Project ID: plumID:21.028
Source: alanine/deepTDA_enhanced_sampling/plumed.dat
Originally used with PLUMED version: 2.7
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. 

phiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17

x1The DISTANCE action with label x1 calculates the following quantities:
 Quantity   
 Type   
 Description  
x1
scalar
the DISTANCE between this pair of atoms: 
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
x2The DISTANCE action with label x2 calculates the following quantities:
 Quantity   
 Type   
 Description  
x2
scalar
the DISTANCE between this pair of atoms: 
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
x3The DISTANCE action with label x3 calculates the following quantities:
 Quantity   
 Type   
 Description  
x3
scalar
the DISTANCE between this pair of atoms: 
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
x4The DISTANCE action with label x4 calculates the following quantities:
 Quantity   
 Type   
 Description  
x4
scalar
the DISTANCE between this pair of atoms: 
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
x5The DISTANCE action with label x5 calculates the following quantities:
 Quantity   
 Type   
 Description  
x5
scalar
the DISTANCE between this pair of atoms: 
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
x6The DISTANCE action with label x6 calculates the following quantities:
 Quantity   
 Type   
 Description  
x6
scalar
the DISTANCE between this pair of atoms: 
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
x7The DISTANCE action with label x7 calculates the following quantities:
 Quantity   
 Type   
 Description  
x7
scalar
the DISTANCE between this pair of atoms: 
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
x8The DISTANCE action with label x8 calculates the following quantities:
 Quantity   
 Type   
 Description  
x8
scalar
the DISTANCE between this pair of atoms: 
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
x9The DISTANCE action with label x9 calculates the following quantities:
 Quantity   
 Type   
 Description  
x9
scalar
the DISTANCE between this pair of atoms: 
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
x10The DISTANCE action with label x10 calculates the following quantities:
 Quantity   
 Type   
 Description  
x10
scalar
the DISTANCE between this pair of atoms: 
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
x11The DISTANCE action with label x11 calculates the following quantities:
 Quantity   
 Type   
 Description  
x11
scalar
the DISTANCE between this pair of atoms: 
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
x12The DISTANCE action with label x12 calculates the following quantities:
 Quantity   
 Type   
 Description  
x12
scalar
the DISTANCE between this pair of atoms: 
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
x13The DISTANCE action with label x13 calculates the following quantities:
 Quantity   
 Type   
 Description  
x13
scalar
the DISTANCE between this pair of atoms: 
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
x14The DISTANCE action with label x14 calculates the following quantities:
 Quantity   
 Type   
 Description  
x14
scalar
the DISTANCE between this pair of atoms: 
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
x15The DISTANCE action with label x15 calculates the following quantities:
 Quantity   
 Type   
 Description  
x15
scalar
the DISTANCE between this pair of atoms: 
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
x16The DISTANCE action with label x16 calculates the following quantities:
 Quantity   
 Type   
 Description  
x16
scalar
the DISTANCE between this pair of atoms: 
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
x17The DISTANCE action with label x17 calculates the following quantities:
 Quantity   
 Type   
 Description  
x17
scalar
the DISTANCE between this pair of atoms: 
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
x18The DISTANCE action with label x18 calculates the following quantities:
 Quantity   
 Type   
 Description  
x18
scalar
the DISTANCE between this pair of atoms: 
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
x19The DISTANCE action with label x19 calculates the following quantities:
 Quantity   
 Type   
 Description  
x19
scalar
the DISTANCE between this pair of atoms: 
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
x20The DISTANCE action with label x20 calculates the following quantities:
 Quantity   
 Type   
 Description  
x20
scalar
the DISTANCE between this pair of atoms: 
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
x21The DISTANCE action with label x21 calculates the following quantities:
 Quantity   
 Type   
 Description  
x21
scalar
the DISTANCE between this pair of atoms: 
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
x22The DISTANCE action with label x22 calculates the following quantities:
 Quantity   
 Type   
 Description  
x22
scalar
the DISTANCE between this pair of atoms: 
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
x23The DISTANCE action with label x23 calculates the following quantities:
 Quantity   
 Type   
 Description  
x23
scalar
the DISTANCE between this pair of atoms: 
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
x24The DISTANCE action with label x24 calculates the following quantities:
 Quantity   
 Type   
 Description  
x24
scalar
the DISTANCE between this pair of atoms: 
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
x25The DISTANCE action with label x25 calculates the following quantities:
 Quantity   
 Type   
 Description  
x25
scalar
the DISTANCE between this pair of atoms: 
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
x26The DISTANCE action with label x26 calculates the following quantities:
 Quantity   
 Type   
 Description  
x26
scalar
the DISTANCE between this pair of atoms: 
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
x27The DISTANCE action with label x27 calculates the following quantities:
 Quantity   
 Type   
 Description  
x27
scalar
the DISTANCE between this pair of atoms: 
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
x28The DISTANCE action with label x28 calculates the following quantities:
 Quantity   
 Type   
 Description  
x28
scalar
the DISTANCE between this pair of atoms: 
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
x29The DISTANCE action with label x29 calculates the following quantities:
 Quantity   
 Type   
 Description  
x29
scalar
the DISTANCE between this pair of atoms: 
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
x30The DISTANCE action with label x30 calculates the following quantities:
 Quantity   
 Type   
 Description  
x30
scalar
the DISTANCE between this pair of atoms: 
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
x31The DISTANCE action with label x31 calculates the following quantities:
 Quantity   
 Type   
 Description  
x31
scalar
the DISTANCE between this pair of atoms: 
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
x32The DISTANCE action with label x32 calculates the following quantities:
 Quantity   
 Type   
 Description  
x32
scalar
the DISTANCE between this pair of atoms: 
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
x33The DISTANCE action with label x33 calculates the following quantities:
 Quantity   
 Type   
 Description  
x33
scalar
the DISTANCE between this pair of atoms: 
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
x34The DISTANCE action with label x34 calculates the following quantities:
 Quantity   
 Type   
 Description  
x34
scalar
the DISTANCE between this pair of atoms: 
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
x35The DISTANCE action with label x35 calculates the following quantities:
 Quantity   
 Type   
 Description  
x35
scalar
the DISTANCE between this pair of atoms: 
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
x36The DISTANCE action with label x36 calculates the following quantities:
 Quantity   
 Type   
 Description  
x36
scalar
the DISTANCE between this pair of atoms: 
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
x37The DISTANCE action with label x37 calculates the following quantities:
 Quantity   
 Type   
 Description  
x37
scalar
the DISTANCE between this pair of atoms: 
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
x38The DISTANCE action with label x38 calculates the following quantities:
 Quantity   
 Type   
 Description  
x38
scalar
the DISTANCE between this pair of atoms: 
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
x39The DISTANCE action with label x39 calculates the following quantities:
 Quantity   
 Type   
 Description  
x39
scalar
the DISTANCE between this pair of atoms: 
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
x40The DISTANCE action with label x40 calculates the following quantities:
 Quantity   
 Type   
 Description  
x40
scalar
the DISTANCE between this pair of atoms: 
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
x41The DISTANCE action with label x41 calculates the following quantities:
 Quantity   
 Type   
 Description  
x41
scalar
the DISTANCE between this pair of atoms: 
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
x42The DISTANCE action with label x42 calculates the following quantities:
 Quantity   
 Type   
 Description  
x42
scalar
the DISTANCE between this pair of atoms: 
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
x43The DISTANCE action with label x43 calculates the following quantities:
 Quantity   
 Type   
 Description  
x43
scalar
the DISTANCE between this pair of atoms: 
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
x44The DISTANCE action with label x44 calculates the following quantities:
 Quantity   
 Type   
 Description  
x44
scalar
the DISTANCE between this pair of atoms: 
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
x45The DISTANCE action with label x45 calculates the following quantities:
 Quantity   
 Type   
 Description  
x45
scalar
the DISTANCE between this pair of atoms: 
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

dTDAThe PYTORCH_MODEL action with label dTDA calculates the following quantities:
 Quantity   
 Type   
 Description  
dTDA.node-0
scalar
Model outputs  This is the 0th of these quantities: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=deepTDA_alanine.pt 
ARG
the input for this action is the scalar output from one or more other actions
=x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11,x12,x13,x14,x15,x16,x17,x18,x19,x20,x21,x22,x23,x24,x25,x26,x27,x28,x29,x30,x31,x32,x33,x34,x35,x36,x37,x38,x39,x40,x41,x42,x43,x44,x45

#DEFINE OPES CALCULATION
opesThe OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential
opes.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff
scalar
effective sample size
opes.nker
scalar
total number of compressed kernels used to represent the bias: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=dTDA.node-0
  
PACE
the frequency for kernel deposition
=500
  
SIGMA
 the initial widths of the kernels
=0.20
  
BARRIER
the free energy barrier to be overcome
=30
...
opes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=dTDA.node-0
  
PACE
the frequency for kernel deposition
=500
  
SIGMA
 the initial widths of the kernels
=0.20
  
BARRIER
the free energy barrier to be overcome
=30
 
TEMP
 temperature
=-1 
COMPRESSION_THRESHOLD
 merge kernels if closer than this threshold, in units of sigma
=1 
FILE
 a file in which the list of all deposited kernels is stored
=KERNELS
...

# print the values on colvar
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=phi,psi,dTDA.node-0,opes 
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