PLUMED-NEST

Project ID: plumID:24.019
Source: ala10/5-adaptive/opes/11/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
pair1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,15
The DISTANCE action with label pair1 calculates the following quantities:
 Quantity   
 Description  
pair1.value
the DISTANCE between this pair of atomspair2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,25
The DISTANCE action with label pair2 calculates the following quantities:
 Quantity   
 Description  
pair2.value
the DISTANCE between this pair of atomspair3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,35
The DISTANCE action with label pair3 calculates the following quantities:
 Quantity   
 Description  
pair3.value
the DISTANCE between this pair of atomspair4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,45
The DISTANCE action with label pair4 calculates the following quantities:
 Quantity   
 Description  
pair4.value
the DISTANCE between this pair of atomspair5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,55
The DISTANCE action with label pair5 calculates the following quantities:
 Quantity   
 Description  
pair5.value
the DISTANCE between this pair of atomspair6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,65
The DISTANCE action with label pair6 calculates the following quantities:
 Quantity   
 Description  
pair6.value
the DISTANCE between this pair of atomspair7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,75
The DISTANCE action with label pair7 calculates the following quantities:
 Quantity   
 Description  
pair7.value
the DISTANCE between this pair of atomspair8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,85
The DISTANCE action with label pair8 calculates the following quantities:
 Quantity   
 Description  
pair8.value
the DISTANCE between this pair of atomspair9: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,95
The DISTANCE action with label pair9 calculates the following quantities:
 Quantity   
 Description  
pair9.value
the DISTANCE between this pair of atomspair10: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,25
The DISTANCE action with label pair10 calculates the following quantities:
 Quantity   
 Description  
pair10.value
the DISTANCE between this pair of atomspair11: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,35
The DISTANCE action with label pair11 calculates the following quantities:
 Quantity   
 Description  
pair11.value
the DISTANCE between this pair of atomspair12: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,45
The DISTANCE action with label pair12 calculates the following quantities:
 Quantity   
 Description  
pair12.value
the DISTANCE between this pair of atomspair13: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,55
The DISTANCE action with label pair13 calculates the following quantities:
 Quantity   
 Description  
pair13.value
the DISTANCE between this pair of atomspair14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,65
The DISTANCE action with label pair14 calculates the following quantities:
 Quantity   
 Description  
pair14.value
the DISTANCE between this pair of atomspair15: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,75
The DISTANCE action with label pair15 calculates the following quantities:
 Quantity   
 Description  
pair15.value
the DISTANCE between this pair of atomspair16: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,85
The DISTANCE action with label pair16 calculates the following quantities:
 Quantity   
 Description  
pair16.value
the DISTANCE between this pair of atomspair17: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,95
The DISTANCE action with label pair17 calculates the following quantities:
 Quantity   
 Description  
pair17.value
the DISTANCE between this pair of atomspair18: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,35
The DISTANCE action with label pair18 calculates the following quantities:
 Quantity   
 Description  
pair18.value
the DISTANCE between this pair of atomspair19: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,45
The DISTANCE action with label pair19 calculates the following quantities:
 Quantity   
 Description  
pair19.value
the DISTANCE between this pair of atomspair20: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,55
The DISTANCE action with label pair20 calculates the following quantities:
 Quantity   
 Description  
pair20.value
the DISTANCE between this pair of atomspair21: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,65
The DISTANCE action with label pair21 calculates the following quantities:
 Quantity   
 Description  
pair21.value
the DISTANCE between this pair of atomspair22: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,75
The DISTANCE action with label pair22 calculates the following quantities:
 Quantity   
 Description  
pair22.value
the DISTANCE between this pair of atomspair23: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,85
The DISTANCE action with label pair23 calculates the following quantities:
 Quantity   
 Description  
pair23.value
the DISTANCE between this pair of atomspair24: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,95
The DISTANCE action with label pair24 calculates the following quantities:
 Quantity   
 Description  
pair24.value
the DISTANCE between this pair of atomspair25: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=35,45
The DISTANCE action with label pair25 calculates the following quantities:
 Quantity   
 Description  
pair25.value
the DISTANCE between this pair of atomspair26: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=35,55
The DISTANCE action with label pair26 calculates the following quantities:
 Quantity   
 Description  
pair26.value
the DISTANCE between this pair of atomspair27: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=35,65
The DISTANCE action with label pair27 calculates the following quantities:
 Quantity   
 Description  
pair27.value
the DISTANCE between this pair of atomspair28: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=35,75
The DISTANCE action with label pair28 calculates the following quantities:
 Quantity   
 Description  
pair28.value
the DISTANCE between this pair of atomspair29: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=35,85
The DISTANCE action with label pair29 calculates the following quantities:
 Quantity   
 Description  
pair29.value
the DISTANCE between this pair of atomspair30: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=35,95
The DISTANCE action with label pair30 calculates the following quantities:
 Quantity   
 Description  
pair30.value
the DISTANCE between this pair of atomspair31: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,55
The DISTANCE action with label pair31 calculates the following quantities:
 Quantity   
 Description  
pair31.value
the DISTANCE between this pair of atomspair32: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,65
The DISTANCE action with label pair32 calculates the following quantities:
 Quantity   
 Description  
pair32.value
the DISTANCE between this pair of atomspair33: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,75
The DISTANCE action with label pair33 calculates the following quantities:
 Quantity   
 Description  
pair33.value
the DISTANCE between this pair of atomspair34: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,85
The DISTANCE action with label pair34 calculates the following quantities:
 Quantity   
 Description  
pair34.value
the DISTANCE between this pair of atomspair35: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,95
The DISTANCE action with label pair35 calculates the following quantities:
 Quantity   
 Description  
pair35.value
the DISTANCE between this pair of atomspair36: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=55,65
The DISTANCE action with label pair36 calculates the following quantities:
 Quantity   
 Description  
pair36.value
the DISTANCE between this pair of atomspair37: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=55,75
The DISTANCE action with label pair37 calculates the following quantities:
 Quantity   
 Description  
pair37.value
the DISTANCE between this pair of atomspair38: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=55,85
The DISTANCE action with label pair38 calculates the following quantities:
 Quantity   
 Description  
pair38.value
the DISTANCE between this pair of atomspair39: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=55,95
The DISTANCE action with label pair39 calculates the following quantities:
 Quantity   
 Description  
pair39.value
the DISTANCE between this pair of atomspair40: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=65,75
The DISTANCE action with label pair40 calculates the following quantities:
 Quantity   
 Description  
pair40.value
the DISTANCE between this pair of atomspair41: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=65,85
The DISTANCE action with label pair41 calculates the following quantities:
 Quantity   
 Description  
pair41.value
the DISTANCE between this pair of atomspair42: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=65,95
The DISTANCE action with label pair42 calculates the following quantities:
 Quantity   
 Description  
pair42.value
the DISTANCE between this pair of atomspair43: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=75,85
The DISTANCE action with label pair43 calculates the following quantities:
 Quantity   
 Description  
pair43.value
the DISTANCE between this pair of atomspair44: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=75,95
The DISTANCE action with label pair44 calculates the following quantities:
 Quantity   
 Description  
pair44.value
the DISTANCE between this pair of atomspair45: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=85,95
The DISTANCE action with label pair45 calculates the following quantities:
 Quantity   
 Description  
pair45.value
the DISTANCE between this pair of atomspsi-1: 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. 
The TORSION action with label psi-1 calculates the following quantities:
 Quantity   
 Description  
psi-1.value
the TORSION involving these atomssinpsi-1: 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
The CUSTOM action with label sinpsi-1 calculates the following quantities:
 Quantity   
 Description  
sinpsi-1.value
an arbitrary functioncospsi-1: 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
The CUSTOM action with label cospsi-1 calculates the following quantities:
 Quantity   
 Description  
cospsi-1.value
an arbitrary functionphi-2: 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. 
The TORSION action with label phi-2 calculates the following quantities:
 Quantity   
 Description  
phi-2.value
the TORSION involving these atomssinphi-2: 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
The CUSTOM action with label sinphi-2 calculates the following quantities:
 Quantity   
 Description  
sinphi-2.value
an arbitrary functioncosphi-2: 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
The CUSTOM action with label cosphi-2 calculates the following quantities:
 Quantity   
 Description  
cosphi-2.value
an arbitrary functionphi-3: 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. 
The TORSION action with label phi-3 calculates the following quantities:
 Quantity   
 Description  
phi-3.value
the TORSION involving these atomssinphi-3: 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
The CUSTOM action with label sinphi-3 calculates the following quantities:
 Quantity   
 Description  
sinphi-3.value
an arbitrary functioncosphi-3: 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
The CUSTOM action with label cosphi-3 calculates the following quantities:
 Quantity   
 Description  
cosphi-3.value
an arbitrary functionphi-4: 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. 
The TORSION action with label phi-4 calculates the following quantities:
 Quantity   
 Description  
phi-4.value
the TORSION involving these atomssinphi-4: 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
The CUSTOM action with label sinphi-4 calculates the following quantities:
 Quantity   
 Description  
sinphi-4.value
an arbitrary functioncosphi-4: 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
The CUSTOM action with label cosphi-4 calculates the following quantities:
 Quantity   
 Description  
cosphi-4.value
an arbitrary functionphi-5: 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. 
The TORSION action with label phi-5 calculates the following quantities:
 Quantity   
 Description  
phi-5.value
the TORSION involving these atomssinphi-5: 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
The CUSTOM action with label sinphi-5 calculates the following quantities:
 Quantity   
 Description  
sinphi-5.value
an arbitrary functioncosphi-5: 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
The CUSTOM action with label cosphi-5 calculates the following quantities:
 Quantity   
 Description  
cosphi-5.value
an arbitrary functionphi-6: 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. 
The TORSION action with label phi-6 calculates the following quantities:
 Quantity   
 Description  
phi-6.value
the TORSION involving these atomssinphi-6: 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
The CUSTOM action with label sinphi-6 calculates the following quantities:
 Quantity   
 Description  
sinphi-6.value
an arbitrary functioncosphi-6: 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
The CUSTOM action with label cosphi-6 calculates the following quantities:
 Quantity   
 Description  
cosphi-6.value
an arbitrary functionphi-7: 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. 
The TORSION action with label phi-7 calculates the following quantities:
 Quantity   
 Description  
phi-7.value
the TORSION involving these atomssinphi-7: 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
The CUSTOM action with label sinphi-7 calculates the following quantities:
 Quantity   
 Description  
sinphi-7.value
an arbitrary functioncosphi-7: 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
The CUSTOM action with label cosphi-7 calculates the following quantities:
 Quantity   
 Description  
cosphi-7.value
an arbitrary functionphi-8: 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. 
The TORSION action with label phi-8 calculates the following quantities:
 Quantity   
 Description  
phi-8.value
the TORSION involving these atomssinphi-8: 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
The CUSTOM action with label sinphi-8 calculates the following quantities:
 Quantity   
 Description  
sinphi-8.value
an arbitrary functioncosphi-8: 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
The CUSTOM action with label cosphi-8 calculates the following quantities:
 Quantity   
 Description  
cosphi-8.value
an arbitrary functionphi-9: 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. 
The TORSION action with label phi-9 calculates the following quantities:
 Quantity   
 Description  
phi-9.value
the TORSION involving these atomssinphi-9: 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
The CUSTOM action with label sinphi-9 calculates the following quantities:
 Quantity   
 Description  
sinphi-9.value
an arbitrary functioncosphi-9: 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

The CUSTOM action with label cosphi-9 calculates the following quantities:
 Quantity   
 Description  
cosphi-9.value
an arbitrary functionpsi-2: 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. 
The TORSION action with label psi-2 calculates the following quantities:
 Quantity   
 Description  
psi-2.value
the TORSION involving these atomssinpsi-2: 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
The CUSTOM action with label sinpsi-2 calculates the following quantities:
 Quantity   
 Description  
sinpsi-2.value
an arbitrary functioncospsi-2: 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
The CUSTOM action with label cospsi-2 calculates the following quantities:
 Quantity   
 Description  
cospsi-2.value
an arbitrary functionpsi-3: 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. 
The TORSION action with label psi-3 calculates the following quantities:
 Quantity   
 Description  
psi-3.value
the TORSION involving these atomssinpsi-3: 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
The CUSTOM action with label sinpsi-3 calculates the following quantities:
 Quantity   
 Description  
sinpsi-3.value
an arbitrary functioncospsi-3: 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
The CUSTOM action with label cospsi-3 calculates the following quantities:
 Quantity   
 Description  
cospsi-3.value
an arbitrary functionpsi-4: 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. 
The TORSION action with label psi-4 calculates the following quantities:
 Quantity   
 Description  
psi-4.value
the TORSION involving these atomssinpsi-4: 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
The CUSTOM action with label sinpsi-4 calculates the following quantities:
 Quantity   
 Description  
sinpsi-4.value
an arbitrary functioncospsi-4: 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
The CUSTOM action with label cospsi-4 calculates the following quantities:
 Quantity   
 Description  
cospsi-4.value
an arbitrary functionpsi-5: 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. 
The TORSION action with label psi-5 calculates the following quantities:
 Quantity   
 Description  
psi-5.value
the TORSION involving these atomssinpsi-5: 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
The CUSTOM action with label sinpsi-5 calculates the following quantities:
 Quantity   
 Description  
sinpsi-5.value
an arbitrary functioncospsi-5: 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
The CUSTOM action with label cospsi-5 calculates the following quantities:
 Quantity   
 Description  
cospsi-5.value
an arbitrary functionpsi-6: 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. 
The TORSION action with label psi-6 calculates the following quantities:
 Quantity   
 Description  
psi-6.value
the TORSION involving these atomssinpsi-6: 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
The CUSTOM action with label sinpsi-6 calculates the following quantities:
 Quantity   
 Description  
sinpsi-6.value
an arbitrary functioncospsi-6: 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
The CUSTOM action with label cospsi-6 calculates the following quantities:
 Quantity   
 Description  
cospsi-6.value
an arbitrary functionpsi-7: 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. 
The TORSION action with label psi-7 calculates the following quantities:
 Quantity   
 Description  
psi-7.value
the TORSION involving these atomssinpsi-7: 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
The CUSTOM action with label sinpsi-7 calculates the following quantities:
 Quantity   
 Description  
sinpsi-7.value
an arbitrary functioncospsi-7: 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
The CUSTOM action with label cospsi-7 calculates the following quantities:
 Quantity   
 Description  
cospsi-7.value
an arbitrary functionpsi-8: 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. 
The TORSION action with label psi-8 calculates the following quantities:
 Quantity   
 Description  
psi-8.value
the TORSION involving these atomssinpsi-8: 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
The CUSTOM action with label sinpsi-8 calculates the following quantities:
 Quantity   
 Description  
sinpsi-8.value
an arbitrary functioncospsi-8: 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
The CUSTOM action with label cospsi-8 calculates the following quantities:
 Quantity   
 Description  
cospsi-8.value
an arbitrary functionpsi-9: 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. 
The TORSION action with label psi-9 calculates the following quantities:
 Quantity   
 Description  
psi-9.value
the TORSION involving these atomssinpsi-9: 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
The CUSTOM action with label sinpsi-9 calculates the following quantities:
 Quantity   
 Description  
sinpsi-9.value
an arbitrary functioncospsi-9: 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

The CUSTOM action with label cospsi-9 calculates the following quantities:
 Quantity   
 Description  
cospsi-9.value
an arbitrary functionphi-10: 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. 
The TORSION action with label phi-10 calculates the following quantities:
 Quantity   
 Description  
phi-10.value
the TORSION involving these atomssinphi-10: 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
The CUSTOM action with label sinphi-10 calculates the following quantities:
 Quantity   
 Description  
sinphi-10.value
an arbitrary functioncosphi-10: 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
The CUSTOM action with label cosphi-10 calculates the following quantities:
 Quantity   
 Description  
cosphi-10.value
an arbitrary functiontica0: 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
The COMBINE action with label tica0 calculates the following quantities:
 Quantity   
 Description  
tica0.value
a linear compbinationtica1: 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
The COMBINE action with label tica1 calculates the following quantities:
 Quantity   
 Description  
tica1.value
a linear compbinationalpha: ALPHARMSDProbe the alpha helical content of a protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all
The ALPHARMSD action with label alpha calculates the following quantities:
 Quantity   
 Description  
alpha.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
alpha.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
alpha.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helixrg: 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
The GYRATION action with label rg calculates the following quantities:
 Quantity   
 Description  
rg.value
the radius that was computed from the weightse2e: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,101
The DISTANCE action with label e2e calculates the following quantities:
 Quantity   
 Description  
e2e.value
the DISTANCE between this pair of atomshbond: COORDINATIONCalculate coordination numbers. 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
The COORDINATION action with label hbond calculates the following quantities:
 Quantity   
 Description  
hbond.value
the value of the coordinationopes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. 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
...
The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
opes.nlker
number of kernels in the neighbor list
opes.nlsteps
number of steps from last neighbor list updatePRINTPrint 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