PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:24.017
Source: BRD4/MetaDynamics/lig1/run0/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
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#  plumed.dat for Funnel MetaD in the WTE + PT #
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RESTARTActivate restart. More details

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### DEFINE RADIUS + CALC PROT-LIG VECTOR COMP ###
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The RESTART action with label  calculates somethingMOLINFOThis 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=../whole.pdb
proteinThe GROUP action with label protein calculates the following quantities: Quantity    Type    Description  
protein atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-2121
ligandThe GROUP action with label ligand calculates the following quantities: Quantity    Type    Description  
ligand atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2122-2199
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=protein ENTITY1the atoms that make up a molecule that you wish to align=ligand
WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=ligand AROUNDreference atoms=1586 GROUPBY group atoms so as not to break molecules=78 #random CA close to the binding pocket for pmas_d in chain B
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### DEFINITION_OF_COMs ###
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ligThe COM action with label lig calculates the following quantities: Quantity    Type    Description  
lig atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=ligand
p0The COM action with label p0 calculates the following quantities: Quantity    Type    Description  
p0 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1105,1461,1473,1521
p1The COM action with label p1 calculates the following quantities: Quantity    Type    Description  
p1 atoms virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=824,846,1122,1586,1739,1774

WOThe GROUP action with label WO calculates the following quantities: Quantity    Type    Description  
WO atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2200-33777:3


# Ligand atoms to solvate
G1The GROUP action with label G1 calculates the following quantities: Quantity    Type    Description  
G1 atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2138
G2The GROUP action with label G2 calculates the following quantities: Quantity    Type    Description  
G2 atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2134
G3The GROUP action with label G3 calculates the following quantities: Quantity    Type    Description  
G3 atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=2124

NG1The COORDINATION action with label NG1 calculates the following quantities: Quantity    Type    Description  
NG1 scalar the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G1 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
NG2The COORDINATION action with label NG2 calculates the following quantities: Quantity    Type    Description  
NG2 scalar the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G2 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
NG3The COORDINATION action with label NG3 calculates the following quantities: Quantity    Type    Description  
NG3 scalar the value of the coordination:  COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G3  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

# Protein atoms to solvate
P1The GROUP action with label P1 calculates the following quantities: Quantity    Type    Description  
P1 atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1590 # CYS 95
P2The GROUP action with label P2 calculates the following quantities: Quantity    Type    Description  
P2 atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1647 # TYR 98
P3The GROUP action with label P3 calculates the following quantities: Quantity    Type    Description  
P3 atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=934 # TYR 56
P4The GROUP action with label P4 calculates the following quantities: Quantity    Type    Description  
P4 atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1528 # MET 91


NP1The COORDINATION action with label NP1 calculates the following quantities: Quantity    Type    Description  
NP1 scalar the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P1 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
NP2The COORDINATION action with label NP2 calculates the following quantities: Quantity    Type    Description  
NP2 scalar the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P2 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
NP3The COORDINATION action with label NP3 calculates the following quantities: Quantity    Type    Description  
NP3 scalar the value of the coordination:  COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P3  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
NP4The COORDINATION action with label NP4 calculates the following quantities: Quantity    Type    Description  
NP4 scalar the value of the coordination:  COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P4  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

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### DEFINITION_OF_CVs ###
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# CV1: pp.proj = projection on the axis. The distance from the axis to the origin (along the axis) (biased)
# CV2: pp.ext = orthogonal distance between the ATOM(=lig) to the axis. (not biased - just monitored)
# CV4: CMAP of 5 protein-ligand contacts
# CV3: RMSD just monitored 
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ppThe PROJECTION_ON_AXIS action with label pp calculates the following quantities: Quantity    Type    Description  
pp.proj scalar The value of the projection along the axis
pp.ext scalar The value of the extension from the axis: PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More details AXIS_ATOMSThe atoms that define the direction of the axis of interest=p0,p1 ATOMThe atom whose position we want to project on the axis of interest=lig

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#RMSD WALLS ####
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rmsd_protCAThe RMSD action with label rmsd_protCA calculates the following quantities: Quantity    Type    Description  
rmsd_protCA scalar the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_protCA: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_protCAThe UPPER_WALLS action with label uwall_rmsd_protCA calculates the following quantities: Quantity    Type    Description  
uwall_rmsd_protCA.bias scalar the instantaneous value of the bias potential
uwall_rmsd_protCA.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_protCA ATthe positions of the wall=0.4 KAPPAthe force constant for the wall=200000

rmsd_pocket_1The RMSD action with label rmsd_pocket_1 calculates the following quantities: Quantity    Type    Description  
rmsd_pocket_1 scalar the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_pocket_1: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_pocket_1The UPPER_WALLS action with label uwall_rmsd_pocket_1 calculates the following quantities: Quantity    Type    Description  
uwall_rmsd_pocket_1.bias scalar the instantaneous value of the bias potential
uwall_rmsd_pocket_1.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_1 ATthe positions of the wall=0.25 KAPPAthe force constant for the wall=200000

rmsd_pocket_2The RMSD action with label rmsd_pocket_2 calculates the following quantities: Quantity    Type    Description  
rmsd_pocket_2 scalar the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_pocket_2: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_pocket_2The UPPER_WALLS action with label uwall_rmsd_pocket_2 calculates the following quantities: Quantity    Type    Description  
uwall_rmsd_pocket_2.bias scalar the instantaneous value of the bias potential
uwall_rmsd_pocket_2.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_2 ATthe positions of the wall=0.23 KAPPAthe force constant for the wall=200000

rmsd_pocket_3The RMSD action with label rmsd_pocket_3 calculates the following quantities: Quantity    Type    Description  
rmsd_pocket_3 scalar the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_pocket_3: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_pocket_3The UPPER_WALLS action with label uwall_rmsd_pocket_3 calculates the following quantities: Quantity    Type    Description  
uwall_rmsd_pocket_3.bias scalar the instantaneous value of the bias potential
uwall_rmsd_pocket_3.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_3 ATthe positions of the wall=0.25 KAPPAthe force constant for the wall=200000

rmsd_tailThe RMSD action with label rmsd_tail calculates the following quantities: Quantity    Type    Description  
rmsd_tail scalar the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_tail.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
rmsd_tail: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_tail.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0
uwall_rmsd_tailThe UPPER_WALLS action with label uwall_rmsd_tail calculates the following quantities: Quantity    Type    Description  
uwall_rmsd_tail.bias scalar the instantaneous value of the bias potential
uwall_rmsd_tail.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_tail ATthe positions of the wall=0.4 KAPPAthe force constant for the wall=200000

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### CMAP #################
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INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=../cmap.dat
# The command:
# INCLUDE FILE=../cmap.dat
# ensures PLUMED loads the contents of the file called ../cmap.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label ../cmap.dat calculates somethingCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1665,2124          SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS2the atoms involved in each of the contacts you wish to calculate=699,2131           SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS3the atoms involved in each of the contacts you wish to calculate=932,2141           SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS4the atoms involved in each of the contacts you wish to calculate=857,2137           SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
LABELa label for the action so that its output can be referenced in the input to other actions=cmapThe CONTACTMAP action with label cmap calculates the following quantities: Quantity    Type    Description  
cmap scalar the sum of all the switching function on all the distances
SUM calculate the sum of all the contacts in the input
... CONTACTMAP

CONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1665,2124          SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS2the atoms involved in each of the contacts you wish to calculate=699,2131           SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS3the atoms involved in each of the contacts you wish to calculate=932,2141           SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS4the atoms involved in each of the contacts you wish to calculate=857,2137           SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
LABELa label for the action so that its output can be referenced in the input to other actions=cmappaThe CONTACTMAP action with label cmappa calculates the following quantities: Quantity    Type    Description  
cmappa.contact-1 scalar By not using SUM or CMDIST each contact will be stored in a component  This is the 1th of these quantities
cmappa.contact-2 scalar By not using SUM or CMDIST each contact will be stored in a component  This is the 2th of these quantities
cmappa.contact-3 scalar By not using SUM or CMDIST each contact will be stored in a component  This is the 3th of these quantities
cmappa.contact-4 scalar By not using SUM or CMDIST each contact will be stored in a component  This is the 4th of these quantities
... CONTACTMAP
# --- End of included input --- 

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# Stiff lig torsions #####
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lig_torsion1The TORSION action with label lig_torsion1 calculates the following quantities: Quantity    Type    Description  
lig_torsion1 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2163,2134,2122,2123
lig_torsion2The TORSION action with label lig_torsion2 calculates the following quantities: Quantity    Type    Description  
lig_torsion2 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2147,2137,2163,2133
lig_torsion3The TORSION action with label lig_torsion3 calculates the following quantities: Quantity    Type    Description  
lig_torsion3 scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2127,2152,2149,2148

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### FUNNEL_PARAMETERS ###
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s_centThe CONSTANT action with label s_cent calculates the following quantities: Quantity    Type    Description  
s_cent scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=2.6                              # INFLEXION
s_cent: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=2.6                              # INFLEXION  NROWS=0 NCOLS=0
beta_centThe CONSTANT action with label beta_cent calculates the following quantities: Quantity    Type    Description  
beta_cent scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.8                            # STEEPNESS
beta_cent: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.8                            # STEEPNESS  NROWS=0 NCOLS=0
wall_widthThe CONSTANT action with label wall_width calculates the following quantities: Quantity    Type    Description  
wall_width scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.1                                  # WIDTH (h)
wall_width: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.1                                  # WIDTH (h)  NROWS=0 NCOLS=0
wall_bufferThe CONSTANT action with label wall_buffer calculates the following quantities: Quantity    Type    Description  
wall_buffer scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=0.25                                 # BUFFER (f, total width = WIDTH + BUFFER)
wall_buffer: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=0.25                                 # BUFFER (f, total width = WIDTH + BUFFER)  NROWS=0 NCOLS=0
lwallThe LOWER_WALLS action with label lwall calculates the following quantities: Quantity    Type    Description  
lwall.bias scalar the instantaneous value of the bias potential
lwall.force2 scalar the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=1.4 KAPPAthe force constant for the wall=2000         # Lower Wall 
uwallThe UPPER_WALLS action with label uwall calculates the following quantities: Quantity    Type    Description  
uwall.bias scalar the instantaneous value of the bias potential
uwall.force2 scalar the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=3.3 KAPPAthe force constant for the wall=2000     # Upper Wall 

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########### CALCULATE FUNNEL #######
# Returns the radius of the funnel
# at the current value of the cv
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MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
    LABELa label for the action so that its output can be referenced in the input to other actions=wall_centerThe MATHEVAL action with label wall_center calculates the following quantities: Quantity    Type    Description  
wall_center scalar an arbitrary function
    ARGthe values input to this function=pp.proj,s_cent,beta_cent,wall_width,wall_buffer
    VARthe names to give each of the arguments in the function=s,sc,b,h,f
    FUNCthe function you wish to evaluate=h*(1./(1.+exp(b*(s-sc))))+f
    PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

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##### POTENTIAL_PARAMETERS #####
################################
scalingThe CONSTANT action with label scaling calculates the following quantities: Quantity    Type    Description  
scaling scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=1.0
scaling: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=1.0  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0
springThe CONSTANT action with label spring calculates the following quantities: Quantity    Type    Description  
spring scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions This action has hidden defaults. More details VALUESthe numbers that are in your constant value=10000.0
spring: CONSTANTCreate a constant value that can be passed to actions This action uses the defaults shown here. More details VALUESthe numbers that are in your constant value=10000.0  NROWS the number of rows in your input matrix=0 NCOLS the number of columns in your matrix=0

################################
####### DEFINE_POTENTIAL #######
################################
MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
    LABELa label for the action so that its output can be referenced in the input to other actions=wall_biasThe MATHEVAL action with label wall_bias calculates the following quantities: Quantity    Type    Description  
wall_bias scalar an arbitrary function
    ARGthe values input to this function=pp.ext,spring,wall_center,scaling
    VARthe names to give each of the arguments in the function=z,k,zc,sf
    FUNCthe function you wish to evaluate=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf)
    PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL
finalbiasThe BIASVALUE action with label finalbias calculates the following quantities: Quantity    Type    Description  
finalbias.bias scalar the instantaneous value of the bias potential
finalbias.wall_bias_bias scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named wall_bias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=wall_bias

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eneThe ENERGY action with label ene calculates the following quantities: Quantity    Type    Description  
ene scalar the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details

METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities: Quantity    Type    Description  
metad.bias scalar the instantaneous value of the bias potential
metad.rbias scalar the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct scalar the reweighting factor c(t).
  ARGthe labels of the scalars on which the bias will act=pp.proj,cmap
  SIGMAthe widths of the Gaussian hills=0.07,0.15
  PACEthe frequency for hill addition=1000
  HEIGHTthe heights of the Gaussian hills=1.5
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  GRID_MINthe lower bounds for the grid=0.0,0.0
  GRID_MAXthe upper bounds for the grid=3.8,5.0
  GRID_BINthe number of bins for the grid=100,50
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=metad
  ARGthe labels of the scalars on which the bias will act=pp.proj,cmap
  SIGMAthe widths of the Gaussian hills=0.07,0.15
  PACEthe frequency for hill addition=1000
  HEIGHTthe heights of the Gaussian hills=1.5
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  GRID_MINthe lower bounds for the grid=0.0,0.0
  GRID_MAXthe upper bounds for the grid=3.8,5.0
  GRID_BINthe number of bins for the grid=100,50
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 FILE a file in which the list of added hills is stored=HILLS
... METAD


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=500 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f
Quantity	Type	Description
protein	atoms	indices of atoms specified in GROUP
PLUMED-NEST-TEST-SITE

The public repository of the PLUMED consortium
