PLUMED-NEST by plumed-nest

Project ID: plumID:24.019
Source: ala10/5-adaptive/opes/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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=input.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=1-104
pair1The DISTANCE action with label pair1 calculates the following quantities: Quantity    Type    Description  
pair1 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=5,15
pair2The DISTANCE action with label pair2 calculates the following quantities: Quantity    Type    Description  
pair2 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=5,25
pair3The DISTANCE action with label pair3 calculates the following quantities: Quantity    Type    Description  
pair3 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=5,35
pair4The DISTANCE action with label pair4 calculates the following quantities: Quantity    Type    Description  
pair4 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=5,45
pair5The DISTANCE action with label pair5 calculates the following quantities: Quantity    Type    Description  
pair5 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=5,55
pair6The DISTANCE action with label pair6 calculates the following quantities: Quantity    Type    Description  
pair6 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=5,65
pair7The DISTANCE action with label pair7 calculates the following quantities: Quantity    Type    Description  
pair7 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=5,75
pair8The DISTANCE action with label pair8 calculates the following quantities: Quantity    Type    Description  
pair8 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=5,85
pair9The DISTANCE action with label pair9 calculates the following quantities: Quantity    Type    Description  
pair9 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=5,95
pair10The DISTANCE action with label pair10 calculates the following quantities: Quantity    Type    Description  
pair10 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=15,25
pair11The DISTANCE action with label pair11 calculates the following quantities: Quantity    Type    Description  
pair11 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=15,35
pair12The DISTANCE action with label pair12 calculates the following quantities: Quantity    Type    Description  
pair12 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=15,45
pair13The DISTANCE action with label pair13 calculates the following quantities: Quantity    Type    Description  
pair13 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=15,55
pair14The DISTANCE action with label pair14 calculates the following quantities: Quantity    Type    Description  
pair14 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=15,65
pair15The DISTANCE action with label pair15 calculates the following quantities: Quantity    Type    Description  
pair15 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=15,75
pair16The DISTANCE action with label pair16 calculates the following quantities: Quantity    Type    Description  
pair16 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=15,85
pair17The DISTANCE action with label pair17 calculates the following quantities: Quantity    Type    Description  
pair17 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=15,95
pair18The DISTANCE action with label pair18 calculates the following quantities: Quantity    Type    Description  
pair18 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=25,35
pair19The DISTANCE action with label pair19 calculates the following quantities: Quantity    Type    Description  
pair19 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=25,45
pair20The DISTANCE action with label pair20 calculates the following quantities: Quantity    Type    Description  
pair20 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=25,55
pair21The DISTANCE action with label pair21 calculates the following quantities: Quantity    Type    Description  
pair21 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=25,65
pair22The DISTANCE action with label pair22 calculates the following quantities: Quantity    Type    Description  
pair22 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=25,75
pair23The DISTANCE action with label pair23 calculates the following quantities: Quantity    Type    Description  
pair23 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=25,85
pair24The DISTANCE action with label pair24 calculates the following quantities: Quantity    Type    Description  
pair24 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=25,95
pair25The DISTANCE action with label pair25 calculates the following quantities: Quantity    Type    Description  
pair25 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=35,45
pair26The DISTANCE action with label pair26 calculates the following quantities: Quantity    Type    Description  
pair26 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=35,55
pair27The DISTANCE action with label pair27 calculates the following quantities: Quantity    Type    Description  
pair27 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=35,65
pair28The DISTANCE action with label pair28 calculates the following quantities: Quantity    Type    Description  
pair28 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=35,75
pair29The DISTANCE action with label pair29 calculates the following quantities: Quantity    Type    Description  
pair29 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=35,85
pair30The DISTANCE action with label pair30 calculates the following quantities: Quantity    Type    Description  
pair30 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=35,95
pair31The DISTANCE action with label pair31 calculates the following quantities: Quantity    Type    Description  
pair31 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=45,55
pair32The DISTANCE action with label pair32 calculates the following quantities: Quantity    Type    Description  
pair32 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=45,65
pair33The DISTANCE action with label pair33 calculates the following quantities: Quantity    Type    Description  
pair33 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=45,75
pair34The DISTANCE action with label pair34 calculates the following quantities: Quantity    Type    Description  
pair34 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=45,85
pair35The DISTANCE action with label pair35 calculates the following quantities: Quantity    Type    Description  
pair35 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=45,95
pair36The DISTANCE action with label pair36 calculates the following quantities: Quantity    Type    Description  
pair36 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=55,65
pair37The DISTANCE action with label pair37 calculates the following quantities: Quantity    Type    Description  
pair37 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=55,75
pair38The DISTANCE action with label pair38 calculates the following quantities: Quantity    Type    Description  
pair38 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=55,85
pair39The DISTANCE action with label pair39 calculates the following quantities: Quantity    Type    Description  
pair39 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=55,95
pair40The DISTANCE action with label pair40 calculates the following quantities: Quantity    Type    Description  
pair40 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=65,75
pair41The DISTANCE action with label pair41 calculates the following quantities: Quantity    Type    Description  
pair41 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=65,85
pair42The DISTANCE action with label pair42 calculates the following quantities: Quantity    Type    Description  
pair42 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=65,95
pair43The DISTANCE action with label pair43 calculates the following quantities: Quantity    Type    Description  
pair43 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=75,85
pair44The DISTANCE action with label pair44 calculates the following quantities: Quantity    Type    Description  
pair44 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=75,95
pair45The DISTANCE action with label pair45 calculates the following quantities: Quantity    Type    Description  
pair45 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=85,95
psi-1The TORSION action with label psi-1 calculates the following quantities: Quantity    Type    Description  
psi-1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-1the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
sinpsi-1The CUSTOM action with label sinpsi-1 calculates the following quantities: Quantity    Type    Description  
sinpsi-1 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-1 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-1The CUSTOM action with label cospsi-1 calculates the following quantities: Quantity    Type    Description  
cospsi-1 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-1 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phi-2The TORSION action with label phi-2 calculates the following quantities: Quantity    Type    Description  
phi-2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
sinphi-2The CUSTOM action with label sinphi-2 calculates the following quantities: Quantity    Type    Description  
sinphi-2 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-2 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-2The CUSTOM action with label cosphi-2 calculates the following quantities: Quantity    Type    Description  
cosphi-2 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-2 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phi-3The TORSION action with label phi-3 calculates the following quantities: Quantity    Type    Description  
phi-3 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-3the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
sinphi-3The CUSTOM action with label sinphi-3 calculates the following quantities: Quantity    Type    Description  
sinphi-3 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-3 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-3The CUSTOM action with label cosphi-3 calculates the following quantities: Quantity    Type    Description  
cosphi-3 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-3 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phi-4The TORSION action with label phi-4 calculates the following quantities: Quantity    Type    Description  
phi-4 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-4the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
sinphi-4The CUSTOM action with label sinphi-4 calculates the following quantities: Quantity    Type    Description  
sinphi-4 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-4 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-4The CUSTOM action with label cosphi-4 calculates the following quantities: Quantity    Type    Description  
cosphi-4 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-4 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phi-5The TORSION action with label phi-5 calculates the following quantities: Quantity    Type    Description  
phi-5 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-5the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
sinphi-5The CUSTOM action with label sinphi-5 calculates the following quantities: Quantity    Type    Description  
sinphi-5 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-5 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-5The CUSTOM action with label cosphi-5 calculates the following quantities: Quantity    Type    Description  
cosphi-5 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-5 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phi-6The TORSION action with label phi-6 calculates the following quantities: Quantity    Type    Description  
phi-6 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-6the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
sinphi-6The CUSTOM action with label sinphi-6 calculates the following quantities: Quantity    Type    Description  
sinphi-6 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-6 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-6The CUSTOM action with label cosphi-6 calculates the following quantities: Quantity    Type    Description  
cosphi-6 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-6 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phi-7The TORSION action with label phi-7 calculates the following quantities: Quantity    Type    Description  
phi-7 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-7the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
sinphi-7The CUSTOM action with label sinphi-7 calculates the following quantities: Quantity    Type    Description  
sinphi-7 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-7 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-7The CUSTOM action with label cosphi-7 calculates the following quantities: Quantity    Type    Description  
cosphi-7 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-7 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phi-8The TORSION action with label phi-8 calculates the following quantities: Quantity    Type    Description  
phi-8 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-8the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
sinphi-8The CUSTOM action with label sinphi-8 calculates the following quantities: Quantity    Type    Description  
sinphi-8 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-8 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-8The CUSTOM action with label cosphi-8 calculates the following quantities: Quantity    Type    Description  
cosphi-8 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-8 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phi-9The TORSION action with label phi-9 calculates the following quantities: Quantity    Type    Description  
phi-9 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-9the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. 
sinphi-9The CUSTOM action with label sinphi-9 calculates the following quantities: Quantity    Type    Description  
sinphi-9 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-9 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-9The CUSTOM action with label cosphi-9 calculates the following quantities: Quantity    Type    Description  
cosphi-9 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-9 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

psi-2The TORSION action with label psi-2 calculates the following quantities: Quantity    Type    Description  
psi-2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
sinpsi-2The CUSTOM action with label sinpsi-2 calculates the following quantities: Quantity    Type    Description  
sinpsi-2 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-2 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-2The CUSTOM action with label cospsi-2 calculates the following quantities: Quantity    Type    Description  
cospsi-2 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-2 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
psi-3The TORSION action with label psi-3 calculates the following quantities: Quantity    Type    Description  
psi-3 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-3the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
sinpsi-3The CUSTOM action with label sinpsi-3 calculates the following quantities: Quantity    Type    Description  
sinpsi-3 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-3 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-3The CUSTOM action with label cospsi-3 calculates the following quantities: Quantity    Type    Description  
cospsi-3 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-3 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
psi-4The TORSION action with label psi-4 calculates the following quantities: Quantity    Type    Description  
psi-4 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-4the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
sinpsi-4The CUSTOM action with label sinpsi-4 calculates the following quantities: Quantity    Type    Description  
sinpsi-4 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-4 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-4The CUSTOM action with label cospsi-4 calculates the following quantities: Quantity    Type    Description  
cospsi-4 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-4 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
psi-5The TORSION action with label psi-5 calculates the following quantities: Quantity    Type    Description  
psi-5 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-5the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
sinpsi-5The CUSTOM action with label sinpsi-5 calculates the following quantities: Quantity    Type    Description  
sinpsi-5 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-5 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-5The CUSTOM action with label cospsi-5 calculates the following quantities: Quantity    Type    Description  
cospsi-5 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-5 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
psi-6The TORSION action with label psi-6 calculates the following quantities: Quantity    Type    Description  
psi-6 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-6the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
sinpsi-6The CUSTOM action with label sinpsi-6 calculates the following quantities: Quantity    Type    Description  
sinpsi-6 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-6 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-6The CUSTOM action with label cospsi-6 calculates the following quantities: Quantity    Type    Description  
cospsi-6 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-6 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
psi-7The TORSION action with label psi-7 calculates the following quantities: Quantity    Type    Description  
psi-7 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-7the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
sinpsi-7The CUSTOM action with label sinpsi-7 calculates the following quantities: Quantity    Type    Description  
sinpsi-7 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-7 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-7The CUSTOM action with label cospsi-7 calculates the following quantities: Quantity    Type    Description  
cospsi-7 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-7 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
psi-8The TORSION action with label psi-8 calculates the following quantities: Quantity    Type    Description  
psi-8 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-8the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
sinpsi-8The CUSTOM action with label sinpsi-8 calculates the following quantities: Quantity    Type    Description  
sinpsi-8 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-8 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-8The CUSTOM action with label cospsi-8 calculates the following quantities: Quantity    Type    Description  
cospsi-8 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-8 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
psi-9The TORSION action with label psi-9 calculates the following quantities: Quantity    Type    Description  
psi-9 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-9the four atoms that are required to calculate the psi dihedral for residue 9. Click here for more information. 
sinpsi-9The CUSTOM action with label sinpsi-9 calculates the following quantities: Quantity    Type    Description  
sinpsi-9 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-9 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cospsi-9The CUSTOM action with label cospsi-9 calculates the following quantities: Quantity    Type    Description  
cospsi-9 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=psi-9 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

phi-10The TORSION action with label phi-10 calculates the following quantities: Quantity    Type    Description  
phi-10 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-10the four atoms that are required to calculate the phi dihedral for residue 10. Click here for more information. 
sinphi-10The CUSTOM action with label sinphi-10 calculates the following quantities: Quantity    Type    Description  
sinphi-10 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-10 FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cosphi-10The CUSTOM action with label cosphi-10 calculates the following quantities: Quantity    Type    Description  
cosphi-10 scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=phi-10 FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
tica0The COMBINE action with label tica0 calculates the following quantities: Quantity    Type    Description  
tica0 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=pair1,pair2,pair3,pair4,pair5,pair6,pair7,pair8,pair9,pair10,pair11,pair12,pair13,pair14,pair15,pair16,pair17,pair18,pair19,pair20,pair21,pair22,pair23,pair24,pair25,pair26,pair27,pair28,pair29,pair30,pair31,pair32,pair33,pair34,pair35,pair36,pair37,pair38,pair39,pair40,pair41,pair42,pair43,pair44,pair45,sinpsi-1,cospsi-1,sinphi-2,cosphi-2,sinphi-3,cosphi-3,sinphi-4,cosphi-4,sinphi-5,cosphi-5,sinphi-6,cosphi-6,sinphi-7,cosphi-7,sinphi-8,cosphi-8,sinphi-9,cosphi-9,sinpsi-2,cospsi-2,sinpsi-3,cospsi-3,sinpsi-4,cospsi-4,sinpsi-5,cospsi-5,sinpsi-6,cospsi-6,sinpsi-7,cospsi-7,sinpsi-8,cospsi-8,sinpsi-9,cospsi-9,sinphi-10,cosphi-10 COEFFICIENTS the coefficients of the arguments in your function=0.45878520838374226,-0.6815614333734615,0.7531199873534522,-0.237838600208029,-1.7725237302409065,1.6128422390868462,0.9731676956871578,-1.3186898651238876,-0.09490914889363498,0.5907897996081745,-0.44109500879678165,-1.29780555506381,2.610420824378029,-0.4888291982128292,-1.5898230650780767,1.0483424917113573,0.37110496686702976,0.15371431666677,1.4798066744222749,-2.0095207274776516,-1.4954444202299186,2.2995879906090457,-0.5942664443281375,-0.27955582586717,0.7177807652419879,-0.07736035468425245,0.1941074605211997,-2.0880309107333206,1.755993638594436,-0.29334282489597185,2.138152842482773,-0.08727542750863332,-0.3584661591675966,-0.5545889231701823,0.23161947574590536,-0.2596333930464869,0.33580210504647956,-0.32897874991000847,-0.030152714752436905,1.4072401742453653,-0.38044996350210947,0.10342267081938522,-0.22752158145220225,-0.0032204098929351542,-0.3473556059275208,-0.00254854002582223,-0.004978294911127841,0.0360211216963392,-0.00513196122561605,-0.012729496074493817,0.05327174576308836,-0.1036293397029794,-0.040946446531515246,0.0312980402262294,-0.05352992538115536,0.05242122886207996,-0.03217696673945797,-0.0563706681165018,-0.04367233336332697,-0.06797151471958346,-0.006328448556341486,0.008794695774383268,-0.0072604084739266595,0.03434778583353606,-0.08946111117475945,-0.09492031217872353,0.0761868736063403,-0.06496591628597252,-0.00788862411707551,-0.06727511409173303,-0.05452399276017694,-0.013025724695818749,-0.03025029799355413,-0.04901583495093996,0.016918969229332028,-0.007597915586481111,-0.022311211774818124,-0.012987189898106448,0.028045143041098695,0.016649580909731735,0.005502719436524739 PARAMETERS the parameters of the arguments in your function=0.38372839,0.66289241,0.91060867,1.12652998,1.32573160,1.51354678,1.69089039,1.85672110,2.01821121,0.38318914,0.64676238,0.87185099,1.09249934,1.29671719,1.48902032,1.66982794,1.84447247,0.38323372,0.64338061,0.86986652,1.08702963,1.29799199,1.49402149,1.68314631,0.38324247,0.64410616,0.86272285,1.08701097,1.29945403,1.50232609,0.38320244,0.63728672,0.86295324,1.08863706,1.30928550,0.38321352,0.64587886,0.87354482,1.11047603,0.38319676,0.64275420,0.88303704,0.38319260,0.65174981,0.38301521,-0.02209226,-0.81743199,-0.78624594,0.10954747,-0.80816870,0.13656246,-0.75490232,0.13368338,-0.78164686,0.11872805,-0.78244709,0.12434511,-0.80413551,0.10664300,-0.78561932,0.11700508,-0.77719369,0.10822025,0.41285861,-0.60949439,0.32909651,-0.38797277,0.32186048,-0.33796143,0.32231677,-0.34795784,0.27478363,-0.24867642,0.34001457,-0.37231472,0.32901420,-0.32131633,0.39968806,-0.46956030,-0.93038751,0.16363428 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
tica1The COMBINE action with label tica1 calculates the following quantities: Quantity    Type    Description  
tica1 scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=pair1,pair2,pair3,pair4,pair5,pair6,pair7,pair8,pair9,pair10,pair11,pair12,pair13,pair14,pair15,pair16,pair17,pair18,pair19,pair20,pair21,pair22,pair23,pair24,pair25,pair26,pair27,pair28,pair29,pair30,pair31,pair32,pair33,pair34,pair35,pair36,pair37,pair38,pair39,pair40,pair41,pair42,pair43,pair44,pair45,sinpsi-1,cospsi-1,sinphi-2,cosphi-2,sinphi-3,cosphi-3,sinphi-4,cosphi-4,sinphi-5,cosphi-5,sinphi-6,cosphi-6,sinphi-7,cosphi-7,sinphi-8,cosphi-8,sinphi-9,cosphi-9,sinpsi-2,cospsi-2,sinpsi-3,cospsi-3,sinpsi-4,cospsi-4,sinpsi-5,cospsi-5,sinpsi-6,cospsi-6,sinpsi-7,cospsi-7,sinpsi-8,cospsi-8,sinpsi-9,cospsi-9,sinphi-10,cosphi-10 COEFFICIENTS the coefficients of the arguments in your function=0.8332504861674326,-0.12376655678586915,-0.05125026710249535,-0.23867479649156492,0.5528703759550545,-0.12398223988156777,-0.4601277269253069,-0.30737761302380934,0.44328542255589587,-0.3887518082351374,0.8360627402908417,-0.478192085125411,-0.30946382812154094,-0.3894108648243526,0.8993860024552865,0.28030464724745774,-0.4977102094106171,-0.24722915103092413,1.22659181732002,-0.3538847933105072,0.14860790517604644,0.08319575398682096,0.056298520692947836,-0.2572466720726419,-1.1743697320843434,-0.28655220944317245,0.633352774017181,-0.7912387125440079,0.7699734536870942,-0.3915420687216509,-0.22008926555154124,-0.5623369705441097,0.7435896681946522,-1.2030049860753664,0.8978362333001741,0.09387701574588064,-0.677989889688182,1.2570934776703138,-0.4250222203613369,0.6232033220921721,-0.6819739771759502,0.1880785256312397,0.08557916047977737,-0.17684617304766373,0.4204440167172054,0.004627642108714586,-0.004885455581907256,0.03589236922278478,-0.013492373586037769,-0.018382748881910743,0.0006825731768412977,-0.2478852332572061,-0.03702724684824637,0.20491829859599672,0.02438274534891358,0.08437568206895471,-0.009590114120581692,0.011943374202168266,0.02246018853744633,0.12129814041102634,0.042679481229578105,0.0709723890253906,0.018999588009141224,0.0816502908822487,-0.08769871290442219,-0.03981701096452041,0.11236359295054114,0.055952273925240915,0.03642232855183963,0.06523125965523956,-0.002465373334908649,0.07944623566316594,-0.0042425561012323885,0.05107538588069659,0.0002041308920131926,0.004396636786672824,-0.0011355641217486888,-0.0334046334936713,0.0009577741105016401,-0.019553641804173943,0.008635248457349153 PARAMETERS the parameters of the arguments in your function=0.38372839,0.66289241,0.91060867,1.12652998,1.32573160,1.51354678,1.69089039,1.85672110,2.01821121,0.38318914,0.64676238,0.87185099,1.09249934,1.29671719,1.48902032,1.66982794,1.84447247,0.38323372,0.64338061,0.86986652,1.08702963,1.29799199,1.49402149,1.68314631,0.38324247,0.64410616,0.86272285,1.08701097,1.29945403,1.50232609,0.38320244,0.63728672,0.86295324,1.08863706,1.30928550,0.38321352,0.64587886,0.87354482,1.11047603,0.38319676,0.64275420,0.88303704,0.38319260,0.65174981,0.38301521,-0.02209226,-0.81743199,-0.78624594,0.10954747,-0.80816870,0.13656246,-0.75490232,0.13368338,-0.78164686,0.11872805,-0.78244709,0.12434511,-0.80413551,0.10664300,-0.78561932,0.11700508,-0.77719369,0.10822025,0.41285861,-0.60949439,0.32909651,-0.38797277,0.32186048,-0.33796143,0.32231677,-0.34795784,0.27478363,-0.24867642,0.34001457,-0.37231472,0.32901420,-0.32131633,0.39968806,-0.46956030,-0.93038751,0.16363428 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
alphaThe ALPHARMSD action with label alpha calculates the following quantities: Quantity    Type    Description  
alpha scalar if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix.  If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all
alpha: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all  NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12 TYPE the manner in which RMSD alignment is performed=DRMSD
# PLUMED interprets the command:
# alpha: ALPHARMSD RESIDUES=all
# as follows (Click the red comment above to revert to the short version of the input):
alpha_rmsdThe SECONDARY_STRUCTURE_RMSD action with label alpha_rmsd calculates the following quantities: Quantity    Type    Description  
alpha_rmsd vector a vector containing the rmsd distance between each of the residue segments and the reference structure: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT2this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 SEGMENT3this is the lists of atoms in the segment that are being considered=10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT4this is the lists of atoms in the segment that are being considered=15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=0.733,0.519,5.298,1.763,0.81,4.301,3.166,0.543,4.881,1.527,-0.045,3.053,1.646,0.436,1.928,1.18,-1.312,3.254,0.924,-2.203,2.126,0.65,-3.626,2.626,-0.239,-1.711,1.261,-0.19,-1.815,0.032,-1.28,-1.172,1.891,-2.416,-0.661,1.127,-3.548,-0.217,2.056,-1.964,0.529,0.276,-2.364,0.659,-0.88,-1.13,1.391,0.856,-0.62,2.565,0.148,0.228,3.439,1.077,0.231,2.129,-1.032,0.179,2.733,-2.099,1.028,1.084,-0.833,1.872,0.593,-1.919,2.85,-0.462,-1.397,1.02,0.02,-3.049,1.317,0.227,-4.224,-0.051,-0.684,-2.696,-0.927,-1.261,-3.713,-1.933,-2.219,-3.074,-1.663,-0.171,-4.475,-1.916,-0.296,-5.673 ATOMSthis is the full list of atoms that we are investigating=1,5,7,11,12,13,15,17,21,22,23,25,27,31,32,33,35,37,41,42,43,45,47,51,52,53,55,57,61,62,63,65,67,71,72,73,75,77,81,82,83,85,87,91,92,93,95,97,101,102 TYPE the manner in which RMSD alignment is performed=DRMSD
alpha_ltThe LESS_THAN action with label alpha_lt calculates the following quantities: Quantity    Type    Description  
alpha_lt vector the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=alpha_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.08 D_0=0.0 NN=8 MM=12}
alphaThe SUM action with label alpha calculates the following quantities: Quantity    Type    Description  
alpha scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- rgThe GYRATION action with label rg calculates the following quantities: Quantity    Type    Description  
rg scalar the radius of gyration: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-104
e2eThe DISTANCE action with label e2e calculates the following quantities: Quantity    Type    Description  
e2e 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=11,101
hbondThe COORDINATION action with label hbond calculates the following quantities: Quantity    Type    Description  
hbond scalar the value of the coordination: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=12,22,32,42,52,62 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=44,54,64,74,84,94 R_0The r_0 parameter of the switching function=0.25 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc
hbond: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=12,22,32,42,52,62 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=44,54,64,74,84,94 R_0The r_0 parameter of the switching function=0.25 PAIR Pair only 1st element of the 1st group with 1st element in the second, etc  D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
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
opes.nlker scalar number of kernels in the neighbor list
opes.nlsteps scalar number of steps from last neighbor list update: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
    ARGthe labels of the scalars on which the bias will act=tica0,tica1
    PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=15
    SIGMA the initial widths of the kernels=0.41398808330524944,0.23241666132297903
    STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=STATE
    STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=STATE
    NLIST use neighbor list for kernels summation, faster but experimental
    WALKERS_MPI switch on MPI version of multiple walkers
...
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
    ARGthe labels of the scalars on which the bias will act=tica0,tica1
    PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=15
    SIGMA the initial widths of the kernels=0.41398808330524944,0.23241666132297903
    STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=STATE
    STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=STATE
    NLIST use neighbor list for kernels summation, faster but experimental
    WALKERS_MPI switch on MPI version of multiple walkers
 TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=alpha,rg,e2e,hbond,tica0,tica1,opes.* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR
Quantity	Type	Description
pair1	scalar	the DISTANCE between this pair of atoms
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