PLUMED-NEST

Project ID: plumID:22.002
Source: OAMe-G4/plumed.dat
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=GAMBES_log.cpp
#LIGAND/HOST
The LOAD action with label  calculates somethingLC: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=29-34,36-37,39-44,46-49,52-53,55-59,62-71,73-75,77-79,81-83,85-108,116-121,123-135,137,139,144,151-160
The GROUP action with label LC calculates somethingLOW: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=29-68
The GROUP action with label LOW calculates somethingCAL: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=29-224
The GROUP action with label CAL calculates somethingL1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=63,65,41,31   #lower exagon
The GROUP action with label L1 calculates somethingL2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=58,42,56,33   #lower exagon
The GROUP action with label L2 calculates somethingHCAL: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=29-160

#GUEST
The GROUP action with label HCAL calculates somethingGC: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-11 #,10-12
The GROUP action with label GC calculates somethingGO: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=12-13
The GROUP action with label GO calculates somethingGBr: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=14
The GROUP action with label GBr calculates somethingGSEL: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2,3,11,14
The GROUP action with label GSEL calculates somethingl1: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2
The GROUP action with label l1 calculates somethingl2: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=3
The GROUP action with label l2 calculates somethingl3: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=11
The GROUP action with label l3 calculates somethingl4: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=14

#Water
The GROUP action with label l4 calculates somethingNa: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=225-233

#Water
The GROUP action with label Na calculates somethingWO: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=234-6533:3

The GROUP action with label WO 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=CAL
FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=conf_template.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
lig: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=GC  #check
The CENTER action with label lig calculates the following quantities:
 Quantity   
 Description  
lig.value
the position of the center of masspock: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=29-68
##DISTANCE ATOMS=pock,lig LABEL=d1  COMPONENTS 

The CENTER action with label pock calculates the following quantities:
 Quantity   
 Description  
pock.value
the position of the center of massv1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.0
The FIXEDATOM action with label v1 calculates somethingv2: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.25
The FIXEDATOM action with label v2 calculates somethingv3: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.5
The FIXEDATOM action with label v3 calculates somethingv4: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.75
The FIXEDATOM action with label v4 calculates somethingv5: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.0
The FIXEDATOM action with label v5 calculates somethingv6: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.25
The FIXEDATOM action with label v6 calculates somethingv7: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.5
The FIXEDATOM action with label v7 calculates somethingv8: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.75
The FIXEDATOM action with label v8 calculates somethingVIRT: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=v1,v2,v3,v4,v5,v6,v7,v8

The GROUP action with label VIRT calculates somethingcyl: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=v1,lig COMPONENTS calculate the x, y and z components of the distance separately and store them as label  #NEW DISTANCE


The DISTANCE action with label cyl calculates the following quantities:
 Quantity   
 Description  
cyl.x
the x-component of the vector connecting the two atoms
cyl.y
the y-component of the vector connecting the two atoms
cyl.z
the z-component of the vector connecting the two atoms
cyl.value
the DISTANCE between this pair of atomscswo1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=l1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cswo1 calculates the following quantities:
 Quantity   
 Description  
cswo1.value
the value of the coordinationcswo2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=l2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cswo2 calculates the following quantities:
 Quantity   
 Description  
cswo2.value
the value of the coordinationcswo3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=l3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cswo3 calculates the following quantities:
 Quantity   
 Description  
cswo3.value
the value of the coordinationcswo4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=l4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cswo4 calculates the following quantities:
 Quantity   
 Description  
cswo4.value
the value of the coordinationcvwo1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cvwo1 calculates the following quantities:
 Quantity   
 Description  
cvwo1.value
the value of the coordinationcvwo2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cvwo2 calculates the following quantities:
 Quantity   
 Description  
cvwo2.value
the value of the coordinationcvwo3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cvwo3 calculates the following quantities:
 Quantity   
 Description  
cvwo3.value
the value of the coordinationcvwo4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cvwo4 calculates the following quantities:
 Quantity   
 Description  
cvwo4.value
the value of the coordinationcvwo5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cvwo5 calculates the following quantities:
 Quantity   
 Description  
cvwo5.value
the value of the coordinationcvwo6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cvwo6 calculates the following quantities:
 Quantity   
 Description  
cvwo6.value
the value of the coordinationcvwo7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5
The COORDINATION action with label cvwo7 calculates the following quantities:
 Quantity   
 Description  
cvwo7.value
the value of the coordinationcvwo8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5

The COORDINATION action with label cvwo8 calculates the following quantities:
 Quantity   
 Description  
cvwo8.value
the value of the coordinationd1: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cswo1 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
an arbitrary functiond2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cswo2 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
an arbitrary functiond3: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cswo3 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
an arbitrary functiond4: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cswo4 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
an arbitrary functiond5: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo1 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
an arbitrary functiond6: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo2 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
an arbitrary functiond7: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo3 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
an arbitrary functiond8: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo4 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
an arbitrary functiond9: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo5 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d9 calculates the following quantities:
 Quantity   
 Description  
d9.value
an arbitrary functiond10: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo6 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d10 calculates the following quantities:
 Quantity   
 Description  
d10.value
an arbitrary functiond11: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo7 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label d11 calculates the following quantities:
 Quantity   
 Description  
d11.value
an arbitrary functiond12: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo8 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

################################

#NEW ANGLE
The MATHEVAL action with label d12 calculates the following quantities:
 Quantity   
 Description  
d12.value
an arbitrary functionlowcal: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=L1 
The CENTER action with label lowcal calculates the following quantities:
 Quantity   
 Description  
lowcal.value
the position of the center of masshighcal: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=L2
The CENTER action with label highcal calculates the following quantities:
 Quantity   
 Description  
highcal.value
the position of the center of massangcalg: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=v3,v5,6,11
The ANGLE action with label angcalg calculates the following quantities:
 Quantity   
 Description  
angcalg.value
the ANGLE involving these atomssang: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=angcalg 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 MATHEVAL action with label sang calculates the following quantities:
 Quantity   
 Description  
sang.value
an arbitrary functioncang: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=angcalg 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

#Funnel
The MATHEVAL action with label cang calculates the following quantities:
 Quantity   
 Description  
cang.value
an arbitrary functionradius: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cyl.x,cyl.y VARthe names to give each of the arguments in the function=x,y FUNCthe function you wish to evaluate=sqrt(x*x+y*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label radius calculates the following quantities:
 Quantity   
 Description  
radius.value
an arbitrary functionfunnel: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=radius,cyl.z VARthe names to give each of the arguments in the function=r,z FUNCthe function you wish to evaluate=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1.) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.value
an arbitrary functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=0 ARGthe arguments on which the bias is acting=funnel KAPPAthe force constant for the wall=2000.0 LABELa label for the action so that its output can be referenced in the input to other actions=funnelwall

# Wall on distance to prevent the protein breaking
The UPPER_WALLS action with label funnelwall calculates the following quantities:
 Quantity   
 Description  
funnelwall.bias
the instantaneous value of the bias potential
funnelwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=1.8 ARGthe arguments on which the bias is acting=cyl.z KAPPAthe force constant for the wall=4000.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=upper_wall

The UPPER_WALLS action with label upper_wall calculates the following quantities:
 Quantity   
 Description  
upper_wall.bias
the instantaneous value of the bias potential
upper_wall.force2
the instantaneous value of the squared force due to this bias potentialautoA: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=modelG4_NN_UW_OW1a.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12
The PYTORCH_MODEL action with label autoA calculates the following quantities:
 Quantity   
 Description  
autoA.node
Model outputsautoB: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=modelG4_NN_UW_OW1b.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12
The PYTORCH_MODEL action with label autoB calculates the following quantities:
 Quantity   
 Description  
autoB.node
Model outputsautoC: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=modelG4_NN_UW_OW1c.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12

The PYTORCH_MODEL action with label autoC calculates the following quantities:
 Quantity   
 Description  
autoC.node
Model outputsAcube: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=autoA.node-0 FUNCthe function you wish to evaluate=x+x^3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label Acube calculates the following quantities:
 Quantity   
 Description  
Acube.value
an arbitrary functionBcube: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=autoB.node-0 FUNCthe function you wish to evaluate=x+x^3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label Bcube calculates the following quantities:
 Quantity   
 Description  
Bcube.value
an arbitrary functionCcube: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=autoC.node-0 FUNCthe function you wish to evaluate=x+x^3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The MATHEVAL action with label Ccube calculates the following quantities:
 Quantity   
 Description  
Ccube.value
an arbitrary functionene: ENERGYCalculate the total potential energy of the simulation box. More details
The ENERGY action with label ene calculates somethingcbhak: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=16 MM=32} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5

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The COORDINATION action with label cbhak calculates the following quantities:
 Quantity   
 Description  
cbhak.value
the value of the coordinationGAMBESLThis action is not part of PLUMED and was included by using a LOAD command More details ...
  LABEL=gambes
  NSTATES=1
  ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z
  FILENAME=dstate
  PACE=500
  BIAS_CUTOFF
  CUTOFF=30
... GAMBESL
COMMITTORDoes a committor analysis. More details ...
  ARGthe labels of the values which is being used to define the committor surface=cyl.z,Acube
  STRIDE the frequency with which the CVs are analyzed=250
  BASIN_LL1List of lower limits for basin #=0.9,-2
  BASIN_UL1List of upper limits for basin #=1.2,3
... COMMITTOR
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f
#PRINT ARG=autoA.node-0,autoB.node-0,swo1,d1.z,swo2,autoC.node-0,funnelwall.bias,upper_wall.bias,opes.bias,opes.rct,swo3,opes.nker,sang,cang,radius,Acube,Bcube,Ccube,swo4,opes.*,ene STRIDE=250 FILE=COLVARmeta FMT=%8.4f
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z,radius,cbhak,ene,gambes.bias STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=COLVARNN FMTthe format that should be used to output real numbers=%8.4f
#PRINT ARG=swo1,swo2,swo3,swo4,vwo1,vwo2,vwo3,vwo4,vwo5,vwo6,vwo7,vwo8,radius,d1.z,ene STRIDE=250 FILE=COLVARNN FMT=%8.4f  
#PRINT ARG=radius,d1.z STRIDE=250 FILE=COLVARbuca FMT=%8.4f
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cyl.z,Acube,gambes.* STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=col_desc FMTthe format that should be used to output real numbers=%8.9f
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=10

ENDPLUMEDTerminate plumed input. More details