Project ID: plumID:21.039
Source: data/chignolin/3_opes_multi_dtica/plumed.dat
Originally used with PLUMED version: 2.8
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. 


####################################
#  >> Chignolin <<
#  OPES Multicanonical (static) + Deep-TICA
####################################

#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

# Deep-TICA CVs
# here deep.node-0 --> Deep-TICA 1
# (Deep-TICA 2 is in ../2_training_cvs/model_2.pt)
deep: 
PYTORCH_MODEL
Load a PyTorch model compiled with TorchScript. More details
 
FILE
Filename of the PyTorch compiled model
=../2_training_cvs/model_1.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

# Define Bias
mc: 
ECV_MULTITHERMAL
Expand a simulation to sample multiple temperatures simultaneously. More details
 
ARG
the label of the internal energy of the system
=ene 
TEMP_MIN
the minimum of the temperature range
=270 
TEMP_MAX
the maximum of the temperature range
=700
# uncomment to enable the static bias (requires to first perform a OPES multithermal simulation)
#static: OPES_EXPANDED PACE=100000000 ARG=mc.* WALKERS_MPI FILE=../1_opes_multi/DELTAFS RESTART=YES 
opes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=deep.node-0 
TEMP
 temperature
=340 
PACE
the frequency for kernel deposition
=500 
BARRIER
the free energy barrier to be overcome
=30 
WALKERS_MPI
 switch on MPI version of multiple walkers
 

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

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=5000