Project ID: plumID:23.009
Source: chignolin/Distance_CV/deepTDA/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
tested onv2.10
tested onmaster
# vim: ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 


####################################
#  >> Chignolin <<
####################################


#generated with gmx editconf -f topol.tpr -o reference.pdb, see https://www.plumed.org/doc-v2.7/user-doc/html/_m_o_l_i_n_f_o.html

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein 
STRUCTURE
a file in pdb format containing a reference structure
=chignolin-ref.pdb

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
=1-166

# Define CVs

# Select Calpha
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
=1-166
CA: 
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
=5,26,47,61,73,88,102,109,123,147
# RMSD
rmsd_ca: 
RMSD
Calculate the RMSD with respect to a reference structure. This action has hidden defaults. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=chignolin-ca.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
# END-TO-END DISTANCE
end: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=5,147
# HBONDS
hbonds: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=23,145 
ATOMS2
the atoms involved in each of the contacts you wish to calculate
=45,120 
ATOMS3
the atoms involved in each of the contacts you wish to calculate
=56,100 
ATOMS4
the atoms involved in each of the contacts you wish to calculate
=56,107 
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.4 NN=6 MM=8} 
SUM
 calculate the sum of all the contacts in the input

ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details


# Define descriptors

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=plumed-descriptors.dat

# Deep-LDA CV
# here deep.node-0 --> Deep-LDA 1
deepLDA: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=model_deep_lda_210distances.ptc 
ARG
the input for this action is the scalar output from one or more other actions
=dd_1-54,dd_1-152,dd_5-7,dd_5-32,dd_5-52,dd_5-81,dd_5-121,dd_5-147,dd_5-158,dd_7-54,dd_7-81,dd_7-82,dd_7-145,dd_7-158,dd_10-52,dd_10-53,dd_10-135,dd_10-147,dd_11-22,dd_11-23,dd_11-54,dd_11-164,dd_11-165,dd_13-32,dd_13-54,dd_13-135,dd_15-18,dd_16-49,dd_18-164,dd_18-165,dd_20-22,dd_20-23,dd_20-32,dd_20-57,dd_20-99,dd_20-120,dd_20-131,dd_20-158,dd_20-165,dd_22-28,dd_22-53,dd_22-164,dd_23-54,dd_23-85,dd_23-92,dd_23-106,dd_23-145,dd_23-160,dd_23-164,dd_26-32,dd_26-55,dd_26-109,dd_26-139,dd_26-166,dd_28-125,dd_31-58,dd_31-63,dd_31-100,dd_31-115,dd_31-144,dd_32-36,dd_32-63,dd_32-66,dd_32-69,dd_34-105,dd_34-128,dd_36-70,dd_36-102,dd_36-105,dd_36-131,dd_36-133,dd_36-137,dd_36-144,dd_37-66,dd_37-69,dd_37-109,dd_39-83,dd_39-137,dd_41-63,dd_41-141,dd_41-144,dd_43-100,dd_43-105,dd_43-120,dd_44-120,dd_44-152,dd_45-47,dd_45-54,dd_45-75,dd_45-147,dd_47-78,dd_49-54,dd_49-71,dd_49-111,dd_49-119,dd_52-57,dd_52-66,dd_52-71,dd_52-83,dd_52-86,dd_52-94,dd_52-144,dd_53-55,dd_53-63,dd_53-69,dd_53-73,dd_53-102,dd_54-66,dd_54-81,dd_54-85,dd_54-120,dd_55-56,dd_55-58,dd_55-69,dd_55-70,dd_56-82,dd_56-105,dd_57-69,dd_57-102,dd_58-94,dd_58-99,dd_61-70,dd_61-71,dd_61-100,dd_61-107,dd_63-70,dd_63-83,dd_63-90,dd_63-105,dd_63-107,dd_63-120,dd_66-78,dd_66-83,dd_66-100,dd_66-107,dd_70-78,dd_70-102,dd_71-75,dd_71-92,dd_71-100,dd_73-88,dd_78-99,dd_78-141,dd_81-92,dd_82-90,dd_82-92,dd_82-94,dd_82-137,dd_83-92,dd_84-86,dd_84-94,dd_84-106,dd_86-98,dd_86-100,dd_88-111,dd_88-113,dd_90-99,dd_90-107,dd_90-109,dd_90-121,dd_90-141,dd_90-153,dd_92-113,dd_92-119,dd_98-107,dd_100-113,dd_102-105,dd_102-139,dd_102-141,dd_105-111,dd_105-123,dd_106-109,dd_106-166,dd_107-139,dd_109-131,dd_113-115,dd_113-121,dd_113-129,dd_113-135,dd_113-141,dd_115-135,dd_119-145,dd_121-125,dd_121-145,dd_125-143,dd_125-160,dd_128-143,dd_128-164,dd_129-134,dd_129-152,dd_129-155,dd_129-160,dd_131-137,dd_131-149,dd_131-162,dd_133-137,dd_133-165,dd_135-139,dd_135-141,dd_135-153,dd_135-158,dd_135-166,dd_137-166,dd_139-165,dd_141-158,dd_144-153,dd_147-155,dd_149-164,dd_149-165,dd_153-160

# Deep-TICA CVs
# here deep.node-0 --> Deep-TICA 1
deepTICA: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=model_deep_tica_210distances.ptc 
ARG
the input for this action is the scalar output from one or more other actions
=dd_1-54,dd_1-152,dd_5-7,dd_5-32,dd_5-52,dd_5-81,dd_5-121,dd_5-147,dd_5-158,dd_7-54,dd_7-81,dd_7-82,dd_7-145,dd_7-158,dd_10-52,dd_10-53,dd_10-135,dd_10-147,dd_11-22,dd_11-23,dd_11-54,dd_11-164,dd_11-165,dd_13-32,dd_13-54,dd_13-135,dd_15-18,dd_16-49,dd_18-164,dd_18-165,dd_20-22,dd_20-23,dd_20-32,dd_20-57,dd_20-99,dd_20-120,dd_20-131,dd_20-158,dd_20-165,dd_22-28,dd_22-53,dd_22-164,dd_23-54,dd_23-85,dd_23-92,dd_23-106,dd_23-145,dd_23-160,dd_23-164,dd_26-32,dd_26-55,dd_26-109,dd_26-139,dd_26-166,dd_28-125,dd_31-58,dd_31-63,dd_31-100,dd_31-115,dd_31-144,dd_32-36,dd_32-63,dd_32-66,dd_32-69,dd_34-105,dd_34-128,dd_36-70,dd_36-102,dd_36-105,dd_36-131,dd_36-133,dd_36-137,dd_36-144,dd_37-66,dd_37-69,dd_37-109,dd_39-83,dd_39-137,dd_41-63,dd_41-141,dd_41-144,dd_43-100,dd_43-105,dd_43-120,dd_44-120,dd_44-152,dd_45-47,dd_45-54,dd_45-75,dd_45-147,dd_47-78,dd_49-54,dd_49-71,dd_49-111,dd_49-119,dd_52-57,dd_52-66,dd_52-71,dd_52-83,dd_52-86,dd_52-94,dd_52-144,dd_53-55,dd_53-63,dd_53-69,dd_53-73,dd_53-102,dd_54-66,dd_54-81,dd_54-85,dd_54-120,dd_55-56,dd_55-58,dd_55-69,dd_55-70,dd_56-82,dd_56-105,dd_57-69,dd_57-102,dd_58-94,dd_58-99,dd_61-70,dd_61-71,dd_61-100,dd_61-107,dd_63-70,dd_63-83,dd_63-90,dd_63-105,dd_63-107,dd_63-120,dd_66-78,dd_66-83,dd_66-100,dd_66-107,dd_70-78,dd_70-102,dd_71-75,dd_71-92,dd_71-100,dd_73-88,dd_78-99,dd_78-141,dd_81-92,dd_82-90,dd_82-92,dd_82-94,dd_82-137,dd_83-92,dd_84-86,dd_84-94,dd_84-106,dd_86-98,dd_86-100,dd_88-111,dd_88-113,dd_90-99,dd_90-107,dd_90-109,dd_90-121,dd_90-141,dd_90-153,dd_92-113,dd_92-119,dd_98-107,dd_100-113,dd_102-105,dd_102-139,dd_102-141,dd_105-111,dd_105-123,dd_106-109,dd_106-166,dd_107-139,dd_109-131,dd_113-115,dd_113-121,dd_113-129,dd_113-135,dd_113-141,dd_115-135,dd_119-145,dd_121-125,dd_121-145,dd_125-143,dd_125-160,dd_128-143,dd_128-164,dd_129-134,dd_129-152,dd_129-155,dd_129-160,dd_131-137,dd_131-149,dd_131-162,dd_133-137,dd_133-165,dd_135-139,dd_135-141,dd_135-153,dd_135-158,dd_135-166,dd_137-166,dd_139-165,dd_141-158,dd_144-153,dd_147-155,dd_149-164,dd_149-165,dd_153-160

#Deep-TDA CV
deepTDA: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=chignolin_distances_two_states_model.pt 
ARG
the input for this action is the scalar output from one or more other actions
=dd_1-54,dd_1-152,dd_5-7,dd_5-32,dd_5-52,dd_5-81,dd_5-121,dd_5-147,dd_5-158,dd_7-54,dd_7-81,dd_7-82,dd_7-145,dd_7-158,dd_10-52,dd_10-53,dd_10-135,dd_10-147,dd_11-22,dd_11-23,dd_11-54,dd_11-164,dd_11-165,dd_13-32,dd_13-54,dd_13-135,dd_15-18,dd_16-49,dd_18-164,dd_18-165,dd_20-22,dd_20-23,dd_20-32,dd_20-57,dd_20-99,dd_20-120,dd_20-131,dd_20-158,dd_20-165,dd_22-28,dd_22-53,dd_22-164,dd_23-54,dd_23-85,dd_23-92,dd_23-106,dd_23-145,dd_23-160,dd_23-164,dd_26-32,dd_26-55,dd_26-109,dd_26-139,dd_26-166,dd_28-125,dd_31-58,dd_31-63,dd_31-100,dd_31-115,dd_31-144,dd_32-36,dd_32-63,dd_32-66,dd_32-69,dd_34-105,dd_34-128,dd_36-70,dd_36-102,dd_36-105,dd_36-131,dd_36-133,dd_36-137,dd_36-144,dd_37-66,dd_37-69,dd_37-109,dd_39-83,dd_39-137,dd_41-63,dd_41-141,dd_41-144,dd_43-100,dd_43-105,dd_43-120,dd_44-120,dd_44-152,dd_45-47,dd_45-54,dd_45-75,dd_45-147,dd_47-78,dd_49-54,dd_49-71,dd_49-111,dd_49-119,dd_52-57,dd_52-66,dd_52-71,dd_52-83,dd_52-86,dd_52-94,dd_52-144,dd_53-55,dd_53-63,dd_53-69,dd_53-73,dd_53-102,dd_54-66,dd_54-81,dd_54-85,dd_54-120,dd_55-56,dd_55-58,dd_55-69,dd_55-70,dd_56-82,dd_56-105,dd_57-69,dd_57-102,dd_58-94,dd_58-99,dd_61-70,dd_61-71,dd_61-100,dd_61-107,dd_63-70,dd_63-83,dd_63-90,dd_63-105,dd_63-107,dd_63-120,dd_66-78,dd_66-83,dd_66-100,dd_66-107,dd_70-78,dd_70-102,dd_71-75,dd_71-92,dd_71-100,dd_73-88,dd_78-99,dd_78-141,dd_81-92,dd_82-90,dd_82-92,dd_82-94,dd_82-137,dd_83-92,dd_84-86,dd_84-94,dd_84-106,dd_86-98,dd_86-100,dd_88-111,dd_88-113,dd_90-99,dd_90-107,dd_90-109,dd_90-121,dd_90-141,dd_90-153,dd_92-113,dd_92-119,dd_98-107,dd_100-113,dd_102-105,dd_102-139,dd_102-141,dd_105-111,dd_105-123,dd_106-109,dd_106-166,dd_107-139,dd_109-131,dd_113-115,dd_113-121,dd_113-129,dd_113-135,dd_113-141,dd_115-135,dd_119-145,dd_121-125,dd_121-145,dd_125-143,dd_125-160,dd_128-143,dd_128-164,dd_129-134,dd_129-152,dd_129-155,dd_129-160,dd_131-137,dd_131-149,dd_131-162,dd_133-137,dd_133-165,dd_135-139,dd_135-141,dd_135-153,dd_135-158,dd_135-166,dd_137-166,dd_139-165,dd_141-158,dd_144-153,dd_147-155,dd_149-164,dd_149-165,dd_153-160

#HLDA
d1: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=23,146 
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d2: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=120,46 
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d3: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=56,101 
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d4: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=56,108 
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d5: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=87,101 
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.15 D_0=0.08 NN=6 MM=8}
d6: 
CONTACTMAP
Calculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details
 
ATOMS1
the atoms involved in each of the contacts you wish to calculate
=72,87 
SWITCH
The switching functions to use for each of the contacts in your map
={RATIONAL R_0=0.12 D_0=0.17 NN=6 MM=8}

hlda: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1.contact-1,d2.contact-1,d3.contact-1,d4.contact-1,d5.contact-1,d6.contact-1 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.6188,0.5975,0.5045,-0.0708,0.0217,0.0140 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. 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
=deepTDA.node-0
  
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
  
TEMP
 temperature
=340
  
BARRIER
the free energy barrier to be overcome
=40
  
SIGMA
 the initial widths of the kernels
=0.2
  
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO
... OPES_METAD



# PRINT

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
=hlda,rmsd_ca,deepLDA.node-0,deepTICA.node-0,deepTDA.node-0,opes.bias 
FILE
the name of the file on which to output these quantities
=COLVARb

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
 
FILE
the name of the file on which to output these quantities
=COLVAR