PLUMED-NEST

Project ID: plumID:24.022
Source: chignolin/infr_metad/template/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

# 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

#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


METADUsed to performed metadynamics on one or more collective variables. 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=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
  ARGthe labels of the scalars on which the bias will act=hlda
  PACEthe frequency for hill addition=10000
  HEIGHTthe heights of the Gaussian hills=1.2
  SIGMAthe widths of the Gaussian hills=0.02
  BIASFACTORuse well tempered metadynamics and use this bias factor=7
  GRID_MINthe lower bounds for the grid=-0.5
  GRID_MAXthe upper bounds for the grid=2.0
  GRID_BINthe number of bins for the grid=125
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] 
... METAD
METADUsed to performed metadynamics on one or more collective variables. 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=metad
  ARGthe labels of the scalars on which the bias will act=hlda
  PACEthe frequency for hill addition=10000
  HEIGHTthe heights of the Gaussian hills=1.2
  SIGMAthe widths of the Gaussian hills=0.02
  BIASFACTORuse well tempered metadynamics and use this bias factor=7
  GRID_MINthe lower bounds for the grid=-0.5
  GRID_MAXthe upper bounds for the grid=2.0
  GRID_BINthe number of bins for the grid=125
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] 
 FILE a file in which the list of added hills is stored=HILLS
... METAD

COMMITTORDoes a committor analysis. More details ...
 ARGthe labels of the values which is being used to define the committor surface=hlda
 STRIDE the frequency with which the CVs are analyzed=10
 BASIN_LL1List of lower limits for basin #=-0.5
 BASIN_UL1List of upper limits for basin #=0.2
... COMMITTOR


# PRINT
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=hlda,end,rmsd_ca,metad.* FILEthe name of the file on which to output these quantities=COLVAR