PLUMED-NEST

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

# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---

protein: 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=1-3232
The GROUP action with label protein 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=protein
The WHOLEMOLECULES action with label  calculates somethingFIT_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=fit_tem.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

WO: 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=3251-47362:3 # water molecules

The GROUP action with label WO calculates somethingG: 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=3236  #ligand selected atom
The GROUP action with label G calculates somethingH: 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=2480   #Bindong pose selected atom

The GROUP action with label H calculates somethinglig: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=3233,3236,3237,3240,3241,3243,3245,3247,3249  #Carbon and Nitrogen atoms of the ligand

# Hydration spots
The CENTER action with label lig calculates the following quantities:
 Quantity   
 Description  
lig.value
the position of the center of massv1:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.710,3.472,4.707
The FIXEDATOM action with label v1 calculates somethingv2:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.600,3.300,4.400
The FIXEDATOM action with label v2 calculates somethingv3:     FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.731,3.025,3.992
The FIXEDATOM action with label v3 calculates somethingv4:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.705,3.084,3.683
The FIXEDATOM action with label v4 calculates somethingv5:     FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.883,3.174,3.461
The FIXEDATOM action with label v5 calculates somethingv6:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.040,3.264,3.306
The FIXEDATOM action with label v6 calculates somethingv7:     FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.239,3.319,3.236
The FIXEDATOM action with label v7 calculates somethingv8:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.485,3.286,3.225
The FIXEDATOM action with label v8 calculates somethingv9:     FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.701,3.182,3.332
The FIXEDATOM action with label v9 calculates somethingv10:     FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.466,3.382,3.446
The FIXEDATOM action with label v10 calculates somethingv11:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.461,3.424,3.659
The FIXEDATOM action with label v11 calculates somethingv12:     FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.495,3.335,3.920
The FIXEDATOM action with label v12 calculates somethingv13:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.295,3.430,3.876
The FIXEDATOM action with label v13 calculates somethingv14:     FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.070,3.450,3.834
The FIXEDATOM action with label v14 calculates somethingv15:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.887,3.241,3.875
The FIXEDATOM action with label v15 calculates somethingv16:    FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=3.815,3.292,4.144

# --- (2) DESCRIPTORS ---
The FIXEDATOM action with label v16 calculates somethingNG: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label NG calculates the following quantities:
 Quantity   
 Description  
NG.value
the value of the coordinationNH: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=H 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=6 MM=10 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20

The COORDINATION action with label NH calculates the following quantities:
 Quantity   
 Description  
NH.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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label cvwo8 calculates the following quantities:
 Quantity   
 Description  
cvwo8.value
the value of the coordinationcvwo9:  COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v9  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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label cvwo9 calculates the following quantities:
 Quantity   
 Description  
cvwo9.value
the value of the coordinationcvwo10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v10 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label cvwo10 calculates the following quantities:
 Quantity   
 Description  
cvwo10.value
the value of the coordinationcvwo11: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v11 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label cvwo11 calculates the following quantities:
 Quantity   
 Description  
cvwo11.value
the value of the coordinationcvwo12: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v12 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label cvwo12 calculates the following quantities:
 Quantity   
 Description  
cvwo12.value
the value of the coordinationcvwo13: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v13 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label cvwo13 calculates the following quantities:
 Quantity   
 Description  
cvwo13.value
the value of the coordinationcvwo14: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v14 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label cvwo14 calculates the following quantities:
 Quantity   
 Description  
cvwo14.value
the value of the coordinationcvwo15: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v15 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label cvwo15 calculates the following quantities:
 Quantity   
 Description  
cvwo15.value
the value of the coordinationcvwo16: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v16 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20

The COORDINATION action with label cvwo16 calculates the following quantities:
 Quantity   
 Description  
cvwo16.value
the value of the coordinationvwo1: 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/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO  #normalized descriptors
The MATHEVAL action with label vwo1 calculates the following quantities:
 Quantity   
 Description  
vwo1.value
an arbitrary functionvwo2: 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/1.5)-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 vwo2 calculates the following quantities:
 Quantity   
 Description  
vwo2.value
an arbitrary functionvwo3: 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/1.5)-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 vwo3 calculates the following quantities:
 Quantity   
 Description  
vwo3.value
an arbitrary functionvwo4: 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/1.5)-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 vwo4 calculates the following quantities:
 Quantity   
 Description  
vwo4.value
an arbitrary functionvwo5: 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/1.5)-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 vwo5 calculates the following quantities:
 Quantity   
 Description  
vwo5.value
an arbitrary functionvwo6: 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/1.5)-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 vwo6 calculates the following quantities:
 Quantity   
 Description  
vwo6.value
an arbitrary functionvwo7: 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/1.5)-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 vwo7 calculates the following quantities:
 Quantity   
 Description  
vwo7.value
an arbitrary functionvwo8: 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/1.5)-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 vwo8 calculates the following quantities:
 Quantity   
 Description  
vwo8.value
an arbitrary functionvwo9: 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=cvwo9 FUNCthe function you wish to evaluate=(x/1.5)-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 vwo9 calculates the following quantities:
 Quantity   
 Description  
vwo9.value
an arbitrary functionvwo10: 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=cvwo10 FUNCthe function you wish to evaluate=(x/1.5)-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 vwo10 calculates the following quantities:
 Quantity   
 Description  
vwo10.value
an arbitrary functionvwo11: 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=cvwo11 FUNCthe function you wish to evaluate=(x/1.5)-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 vwo11 calculates the following quantities:
 Quantity   
 Description  
vwo11.value
an arbitrary functionvwo12: 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=cvwo12 FUNCthe function you wish to evaluate=(x/1.5)-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 vwo12 calculates the following quantities:
 Quantity   
 Description  
vwo12.value
an arbitrary functionvwo13: 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=cvwo13 FUNCthe function you wish to evaluate=(x/1.5)-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 vwo13 calculates the following quantities:
 Quantity   
 Description  
vwo13.value
an arbitrary functionvwo14: 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=cvwo14 FUNCthe function you wish to evaluate=(x/1.5)-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 vwo14 calculates the following quantities:
 Quantity   
 Description  
vwo14.value
an arbitrary functionvwo15: 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=cvwo15 FUNCthe function you wish to evaluate=(x/1.5)-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 vwo15 calculates the following quantities:
 Quantity   
 Description  
vwo15.value
an arbitrary functionvwo16: 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=cvwo16 FUNCthe function you wish to evaluate=(x/1.5)-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 vwo16 calculates the following quantities:
 Quantity   
 Description  
vwo16.value
an arbitrary functionFG: 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=NG FUNCthe function you wish to evaluate=(x/1.5)-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 FG calculates the following quantities:
 Quantity   
 Description  
FG.value
an arbitrary functionFH: 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=NH 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


# ---(3) Funnel ---
The MATHEVAL action with label FH calculates the following quantities:
 Quantity   
 Description  
FH.value
an arbitrary functioncyl: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=v14,lig COMPONENTS calculate the x, y and z components of the distance separately and store them as label
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 atomsradius: 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+0.5*(-1.6+z))*step(-z+1.2)+(r-0.2)*step(z-1.2) 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=10000.0 LABELa label for the action so that its output can be referenced in the input to other actions=funnelwall

# ---(4) Wall on distance to prevent exit of ligand 
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 potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=0.2 ARGthe arguments on which the bias is acting=cyl.z KAPPAthe force constant for the wall=5000.0 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=lower_wall_z

# ---(5) This rmsd restricts the CA momevement of the entire protein
The LOWER_WALLS action with label lower_wall_z calculates the following quantities:
 Quantity   
 Description  
lower_wall_z.bias
the instantaneous value of the bias potential
lower_wall_z.force2
the instantaneous value of the squared force due to this bias potentialrmsdINIT: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=fit_tem.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label rmsdINIT calculates the following quantities:
 Quantity   
 Description  
rmsdINIT.value
the RMSD distance between the instantaneous structure and the reference structure/s that were inputUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsdINIT ATthe positions of the wall=0.09 KAPPAthe force constant for the wall=420000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=rmsdwallINIT 

# --- (6) DEEP-LDA CV ---
The UPPER_WALLS action with label rmsdwallINIT calculates the following quantities:
 Quantity   
 Description  
rmsdwallINIT.bias
the instantaneous value of the bias potential
rmsdwallINIT.force2
the instantaneous value of the squared force due to this bias potentials: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=CV_16V_G_H_1.pt ARGthe labels of the values from which the function is calculated=vwo14,vwo3,vwo5,vwo9,vwo7,vwo10,vwo12,vwo11,vwo6,vwo2,vwo16,vwo1,vwo15,vwo8,vwo13,vwo4,FG,FH
The PYTORCH_MODEL action with label s calculates the following quantities:
 Quantity   
 Description  
s.node
Model outputssw: 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=s.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

# --- (7) DEEP-TICA CV ---

The MATHEVAL action with label sw calculates the following quantities:
 Quantity   
 Description  
sw.value
an arbitrary functiont: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=deeptica_all_lag_0.07model_all.pt ARGthe labels of the values from which the function is calculated=vwo14,vwo3,vwo5,vwo9,vwo7,vwo10,vwo12,vwo11,vwo6,vwo2,vwo16,vwo1,vwo15,vwo8,vwo13,vwo4,FG,FH
The PYTORCH_MODEL action with label t calculates the following quantities:
 Quantity   
 Description  
t.node
Model outputsst: 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=t.node-0 FUNCthe function you wish to evaluate=1*x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

The MATHEVAL action with label st calculates the following quantities:
 Quantity   
 Description  
st.value
an arbitrary functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=1.1 ARGthe arguments on which the bias is acting=st  KAPPAthe force constant for the wall=5000.0 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_st
The UPPER_WALLS action with label upper_st calculates the following quantities:
 Quantity   
 Description  
upper_st.bias
the instantaneous value of the bias potential
upper_st.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=-1.1 ARGthe arguments on which the bias is acting=st KAPPAthe force constant for the wall=5000.0 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=lower_st

# --- (8) EXCLUDED region ____

The LOWER_WALLS action with label lower_st calculates the following quantities:
 Quantity   
 Description  
lower_st.bias
the instantaneous value of the bias potential
lower_st.force2
the instantaneous value of the squared force due to this bias potentialtarget: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cyl.z FUNCthe function you wish to evaluate=step(x-0.6) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# --- (9) OPES flooding  ---

The CUSTOM action with label target calculates the following quantities:
 Quantity   
 Description  
target.value
an arbitrary functionOPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes
  ARGthe labels of the scalars on which the bias will act (a vector must have a single element, e=cyl.z,st
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  PACEthe frequency for kernel deposition=50
  BARRIERthe free energy barrier to be overcome=22
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=target
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
  NLISTIncluding this keyword in the input to this action makes no difference to the calculation performed it was used in older versions of PLUMED and is provided here for back compatibility only
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=500
... OPES_METAD

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 updateCOMMITTORDoes a committor analysis. More details ...
 ARGthe labels of the values which is being used to define the committor surface=cyl.z
 STRIDE the frequency with which the CVs are analyzed=1000
 BASIN_LL1List of lower limits for basin #=1.5
 BASIN_UL1List of upper limits for basin #=1.6
... 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 FMT the format that should be used to output real numbers=%8.4f
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=opes.bias,cyl.z,st STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVARP FMT the format that should be used to output real numbers=%8.4f