Project ID: plumID:22.031
Source: Chignolin/folding/plumed_rate.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 onv2.9
tested onmaster
# vim: ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details.

#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. 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



deepTICA:
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
FILE
Filename of the PyTorch compiled model
=model_tica.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
deepLDA:
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
FILE
Filename of the PyTorch compiled model
=model_lda.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
#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
chi_exc:
CUSTOM
Calculate a combination of variables using a custom expression. More details
ARG
the input to this function
=deepTICA.node-0
FUNC
the function you wish to evaluate
=step(-0.25+x
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO #chi_exc: CUSTOM ARG=deepLDA.node-0 FUNC=step(0.7+x) PERIODIC=NO #chi_exc: CUSTOM ARG=hlda FUNC=step(-0.60+x) PERIODIC=NO
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
=deepTICA.node-0 #ARG=deepLDA.node-0 #ARG=hlda
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
=10
SIGMA
the initial widths of the kernels
=0.05
EXCLUDED_REGION
kernels are not deposited when the action provided here has a nonzero value, see example above
=chi_exc
RESTART
allows per-action setting of restart (YES/NO/AUTO)
=NO #NLIST
STATE_WSTRIDE
number of MD steps between writing the STATE_WFILE
=5000 # EXCLUDED_INTERVAL=0.6,2.5,-1.0,1.0 ... OPES_METAD
COMMITTOR
Does a committor analysis. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=deepTICA.node-0
STRIDE
the frequency with which the CVs are analyzed
=5000
BASIN_LL1
List of lower limits for basin #
=0.3
BASIN_UL1
List of upper limits for basin #
=1.0 ... COMMITTOR
#COMMITTOR ... # ARG=deepLDA.node-0 # STRIDE=5000 # BASIN_LL1=1.3 # BASIN_UL1=1.8 #... COMMITTOR
#COMMITTOR ... # ARG=hlda # STRIDE=5000 # BASIN_LL1=1.5 # BASIN_UL1=1.8 #... COMMITTOR
# PRINT
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=10
ARG
the input for this action is the scalar output from one or more other actions
=opes.bias,hlda,rmsd_ca,deepTICA.node-0,deepLDA.node-0
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
=50
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 #FLUSH STRIDE=5000