PLUMED-NEST

Project ID: plumID:24.029
Source: Chignolin/opes_and_opes_explore/plumed_hlda.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

# vim: ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

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#  >> Chignolin <<
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#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
MOLINFOThis 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 STRUCTUREa file in pdb format containing a reference structure=chignolin-ref.pdb
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-166

# Define CVs

# Select Calpha
PROTEINThe GROUP action with label PROTEIN calculates the following quantities:
 Quantity   
 Type   
 Description  
PROTEIN
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1-166
CAThe GROUP action with label CA calculates the following quantities:
 Quantity   
 Type   
 Description  
CA
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=5,26,47,61,73,88,102,109,123,147
# RMSD
rmsd_caThe RMSD action with label rmsd_ca calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd_ca
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa 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
rmsd_ca: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa 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  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
# END-TO-END DISTANCE
endThe DISTANCE action with label end calculates the following quantities:
 Quantity   
 Type   
 Description  
end
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,147
# HBONDS
hbondsThe CONTACTMAP action with label hbonds calculates the following quantities:
 Quantity   
 Type   
 Description  
hbonds
scalar
the sum of all the switching function on all the distances: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=23,145 ATOMS2the atoms involved in each of the contacts you wish to calculate=45,120 ATOMS3the atoms involved in each of the contacts you wish to calculate=56,100 ATOMS4the atoms involved in each of the contacts you wish to calculate=56,107 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.4 NN=6 MM=8} SUM calculate the sum of all the contacts in the input
eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details


#HLDA
d1The CONTACTMAP action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.contact-1
scalar
By not using SUM or CMDIST each contact will be stored in a component  This is the 1th of these quantities: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=23,146 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d2The CONTACTMAP action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2.contact-1
scalar
By not using SUM or CMDIST each contact will be stored in a component  This is the 1th of these quantities: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=120,46 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d3The CONTACTMAP action with label d3 calculates the following quantities:
 Quantity   
 Type   
 Description  
d3.contact-1
scalar
By not using SUM or CMDIST each contact will be stored in a component  This is the 1th of these quantities: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=56,101 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d4The CONTACTMAP action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4.contact-1
scalar
By not using SUM or CMDIST each contact will be stored in a component  This is the 1th of these quantities: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=56,108 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.3 D_0=0.0 NN=6 MM=8}
d5The CONTACTMAP action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5.contact-1
scalar
By not using SUM or CMDIST each contact will be stored in a component  This is the 1th of these quantities: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=87,101 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.15 D_0=0.08 NN=6 MM=8}
d6The CONTACTMAP action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6.contact-1
scalar
By not using SUM or CMDIST each contact will be stored in a component  This is the 1th of these quantities: CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ATOMS1the atoms involved in each of the contacts you wish to calculate=72,87 SWITCHThe switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.12 D_0=0.17 NN=6 MM=8}

hldaThe COMBINE action with label hlda calculates the following quantities:
 Quantity   
 Type   
 Description  
hlda
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action has hidden defaults. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opesEThe OPES_METAD_EXPLORE action with label opesE calculates the following quantities:
 Quantity   
 Type   
 Description  
opesE.bias
scalar
the instantaneous value of the bias potential
opesE.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesE.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesE.neff
scalar
effective sample size
opesE.nker
scalar
total number of compressed kernels used to represent the bias
  ARGthe labels of the scalars on which the bias will act=hlda
  FILE a file in which the list of all deposited kernels is stored=KernelsE.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressedE.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressedE.Kernels
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=20
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
... OPES_METAD_EXPLORE
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action uses the defaults shown here. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opesE
  ARGthe labels of the scalars on which the bias will act=hlda
  FILE a file in which the list of all deposited kernels is stored=KernelsE.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressedE.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressedE.Kernels
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=20
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
 SIGMA the initial widths of the kernels, divided by the square root of gamma=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE

OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=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
  ARGthe labels of the scalars on which the bias will act=hlda
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=30
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
... OPES_METAD
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes
  ARGthe labels of the scalars on which the bias will act=hlda
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  PACEthe frequency for kernel deposition=500
  TEMP temperature=340
  BARRIERthe free energy barrier to be overcome=30
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD

# PRINT
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 ARGthe labels of the values that you would like to print to the file=hlda,rmsd_ca,opes.bias,opesE.bias FILEthe name of the file on which to output these quantities=COLVARb
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000