PLUMED-NEST-TEST-SITE

Project ID: plumID:23.045
Source: Path-CVs_MetaD/neca-bound/plumed.dat
Originally used with PLUMED version: 2.7.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=FApo.pdb
The MOLINFO action with label  calculates somethingp: PATHMSDThis Colvar calculates path collective variables. More details REFERENCEthe pdb is needed to provide the various milestones=path_rmsd.pdb  LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=122.00
The PATHMSD action with label p calculates the following quantities:
 Quantity   
 Description  
p.sss
the position on the path
p.zzz
the distance from the pathd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1458,3468
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3080,3468
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsH6: ALPHARMSDProbe the alpha helical content of a protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=220-252
The ALPHARMSD action with label H6 calculates the following quantities:
 Quantity   
 Description  
H6.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
H6.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
H6.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdH5: ALPHARMSDProbe the alpha helical content of a protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=198-209

The ALPHARMSD action with label H5 calculates the following quantities:
 Quantity   
 Description  
H5.value
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix
H5.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
H5.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=path_cmap.dat
# The command:
# INCLUDE FILE=path_cmap.dat
# ensures PLUMED loads the contents of the file called path_cmap.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label path_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=3468,3080   REFERENCE1A reference value for a given contact, by default is 0=0.97915123  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=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458   REFERENCE2A reference value for a given contact, by default is 0=0.00041408  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=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438   REFERENCE3A reference value for a given contact, by default is 0=0.02647680  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=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438   REFERENCE4A reference value for a given contact, by default is 0=0.08877594  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=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951   REFERENCE5A reference value for a given contact, by default is 0=0.42785568  SWITCH5The 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=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387   REFERENCE6A reference value for a given contact, by default is 0=0.10367204  SWITCH6The 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=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936   REFERENCE7A reference value for a given contact, by default is 0=0.98727453  SWITCH7The 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=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625    REFERENCE8A reference value for a given contact, by default is 0=0.14748926  SWITCH8The 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=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c1
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP


The CONTACTMAP action with label c1 calculates the following quantities:
 Quantity   
 Description  
c1.contact
By not using SUM or CMDIST each contact will be stored in a component
c1.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate 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=3468,3080   REFERENCE1A reference value for a given contact, by default is 0=0.99076543  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=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458   REFERENCE2A reference value for a given contact, by default is 0=0.00120232  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=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438   REFERENCE3A reference value for a given contact, by default is 0=0.07366488  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=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438   REFERENCE4A reference value for a given contact, by default is 0=0.79523553  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=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951   REFERENCE5A reference value for a given contact, by default is 0=0.28660977  SWITCH5The 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=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387   REFERENCE6A reference value for a given contact, by default is 0=0.33348235  SWITCH6The 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=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936   REFERENCE7A reference value for a given contact, by default is 0=0.96457138  SWITCH7The 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=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625    REFERENCE8A reference value for a given contact, by default is 0=0.12877288  SWITCH8The 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=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c2
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP


The CONTACTMAP action with label c2 calculates the following quantities:
 Quantity   
 Description  
c2.contact
By not using SUM or CMDIST each contact will be stored in a component
c2.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate 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=3468,3080   REFERENCE1A reference value for a given contact, by default is 0=0.97985636  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=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458   REFERENCE2A reference value for a given contact, by default is 0=0.00298822  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=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438   REFERENCE3A reference value for a given contact, by default is 0=0.32581507  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=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438   REFERENCE4A reference value for a given contact, by default is 0=0.97691480  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=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951   REFERENCE5A reference value for a given contact, by default is 0=0.64179803  SWITCH5The 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=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387   REFERENCE6A reference value for a given contact, by default is 0=0.39343434  SWITCH6The 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=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936   REFERENCE7A reference value for a given contact, by default is 0=0.80857049  SWITCH7The 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=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625    REFERENCE8A reference value for a given contact, by default is 0=0.98023826  SWITCH8The 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=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c3
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP


The CONTACTMAP action with label c3 calculates the following quantities:
 Quantity   
 Description  
c3.contact
By not using SUM or CMDIST each contact will be stored in a component
c3.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate 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=3468,3080   REFERENCE1A reference value for a given contact, by default is 0=0.98302451  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=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458   REFERENCE2A reference value for a given contact, by default is 0=0.00222719  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=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438   REFERENCE3A reference value for a given contact, by default is 0=0.28721980  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=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438   REFERENCE4A reference value for a given contact, by default is 0=0.97341515  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=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951   REFERENCE5A reference value for a given contact, by default is 0=0.39377719  SWITCH5The 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=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387   REFERENCE6A reference value for a given contact, by default is 0=0.58032321  SWITCH6The 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=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936   REFERENCE7A reference value for a given contact, by default is 0=0.10151712  SWITCH7The 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=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625    REFERENCE8A reference value for a given contact, by default is 0=0.99945112  SWITCH8The 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=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c4
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

The CONTACTMAP action with label c4 calculates the following quantities:
 Quantity   
 Description  
c4.contact
By not using SUM or CMDIST each contact will be stored in a component
c4.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate 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=3468,3080   REFERENCE1A reference value for a given contact, by default is 0=0.37447568  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=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458   REFERENCE2A reference value for a given contact, by default is 0=0.00700306  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=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438   REFERENCE3A reference value for a given contact, by default is 0=0.47787638  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=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438   REFERENCE4A reference value for a given contact, by default is 0=0.97674738  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=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951   REFERENCE5A reference value for a given contact, by default is 0=0.03917644  SWITCH5The 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=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387   REFERENCE6A reference value for a given contact, by default is 0=0.99881752  SWITCH6The 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=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936   REFERENCE7A reference value for a given contact, by default is 0=0.00122655  SWITCH7The 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=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625    REFERENCE8A reference value for a given contact, by default is 0=0.99974666  SWITCH8The 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=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c5
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

The CONTACTMAP action with label c5 calculates the following quantities:
 Quantity   
 Description  
c5.contact
By not using SUM or CMDIST each contact will be stored in a component
c5.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate 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=3468,3080   REFERENCE1A reference value for a given contact, by default is 0=0.00478415  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=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458   REFERENCE2A reference value for a given contact, by default is 0=0.37643526  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=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438   REFERENCE3A reference value for a given contact, by default is 0=0.96181240  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=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438   REFERENCE4A reference value for a given contact, by default is 0=0.96500778  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=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951   REFERENCE5A reference value for a given contact, by default is 0=0.16431360  SWITCH5The 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=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387   REFERENCE6A reference value for a given contact, by default is 0=0.98327651  SWITCH6The 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=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936   REFERENCE7A reference value for a given contact, by default is 0=0.28874741  SWITCH7The 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=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625    REFERENCE8A reference value for a given contact, by default is 0=0.96352033  SWITCH8The 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=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c6
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP


The CONTACTMAP action with label c6 calculates the following quantities:
 Quantity   
 Description  
c6.contact
By not using SUM or CMDIST each contact will be stored in a component
c6.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate 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=3468,3080   REFERENCE1A reference value for a given contact, by default is 0=0.00064458  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=0.70 NN=8 MM=16}
ATOMS2the atoms involved in each of the contacts you wish to calculate=3468,1458   REFERENCE2A reference value for a given contact, by default is 0=0.93811079  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=0.70 NN=8 MM=16}
ATOMS3the atoms involved in each of the contacts you wish to calculate=3468,1438   REFERENCE3A reference value for a given contact, by default is 0=0.99043541  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=1.65 NN=8 MM=18}
ATOMS4the atoms involved in each of the contacts you wish to calculate=1458,1438   REFERENCE4A reference value for a given contact, by default is 0=0.96998468  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=0.75 NN=6 MM=18}
ATOMS5the atoms involved in each of the contacts you wish to calculate=3566,2951   REFERENCE5A reference value for a given contact, by default is 0=0.03311838  SWITCH5The 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=0.90 NN=8 MM=16}
ATOMS6the atoms involved in each of the contacts you wish to calculate=3566,1387   REFERENCE6A reference value for a given contact, by default is 0=0.99966434  SWITCH6The 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=1.00 NN=10 MM=24}
ATOMS7the atoms involved in each of the contacts you wish to calculate=4418,2936   REFERENCE7A reference value for a given contact, by default is 0=0.06060704  SWITCH7The 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=0.85 NN=8 MM=28}
ATOMS8the atoms involved in each of the contacts you wish to calculate=4418,625    REFERENCE8A reference value for a given contact, by default is 0=0.99816484  SWITCH8The 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=0.67 NN=12 MM=24}
LABELa label for the action so that its output can be referenced in the input to other actions=c7
CMDIST calculate the distance with respect to the provided reference contact map
... CONTACTMAP

# --- End of included input --- The CONTACTMAP action with label c7 calculates the following quantities:
 Quantity   
 Description  
c7.contact
By not using SUM or CMDIST each contact will be stored in a component
c7.value
the sum of all the switching function on all the distancesp1: FUNCPATHMSDThis function calculates path collective variables. More details ARGthe labels of the values from which the function is calculated=c1,c2,c3,c4,c5,c6,c7  LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=3.634


The FUNCPATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.s
the position on the path
p1.z
the distance from the pathmeta: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=p.sss,p1.s SIGMAthe widths of the Gaussian hills=0.1,0.03  HEIGHTthe heights of the Gaussian hills=4 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=15 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300 GRID_MINthe lower bounds for the grid=1,1 GRID_MAXthe upper bounds for the grid=12,7 GRID_WFILEthe file on which to write the grid=GRID_W  GRID_WSTRIDEwrite the grid to a file every N steps=2500000

#Helicity Wall
The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.bias
the instantaneous value of the bias potentiallwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=H6 ATthe positions of the wall=24.8 KAPPAthe force constant for the wall=1500.0

#TM3-TM5 Distances
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentiald3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1519,3047
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1469,2989
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1414,2909
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsuwall1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d3  ATthe positions of the wall=0.75 KAPPAthe force constant for the wall=100.000
The UPPER_WALLS action with label uwall1 calculates the following quantities:
 Quantity   
 Description  
uwall1.bias
the instantaneous value of the bias potential
uwall1.force2
the instantaneous value of the squared force due to this bias potentialuwall2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d4  ATthe positions of the wall=0.625 KAPPAthe force constant for the wall=100.000
The UPPER_WALLS action with label uwall2 calculates the following quantities:
 Quantity   
 Description  
uwall2.bias
the instantaneous value of the bias potential
uwall2.force2
the instantaneous value of the squared force due to this bias potentialuwall3: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d5  ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=100.000
The UPPER_WALLS action with label uwall3 calculates the following quantities:
 Quantity   
 Description  
uwall3.bias
the instantaneous value of the bias potential
uwall3.force2
the instantaneous value of the squared force due to this bias potentialuwallpz: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=p1.z ATthe positions of the wall=0.05 KAPPAthe force constant for the wall=1000.0

The UPPER_WALLS action with label uwallpz calculates the following quantities:
 Quantity   
 Description  
uwallpz.bias
the instantaneous value of the bias potential
uwallpz.force2
the instantaneous value of the squared force due to this bias potentiald6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2936,4418
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsuw: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d6 ATthe positions of the wall=0.65 KAPPAthe force constant for the wall=00.000
The UPPER_WALLS action with label uw calculates the following quantities:
 Quantity   
 Description  
uw.bias
the instantaneous value of the bias potential
uw.force2
the instantaneous value of the squared force due to this bias potentiald7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3468,3332
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomslw: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d7 ATthe positions of the wall=0.7 KAPPAthe force constant for the wall=100.00
The LOWER_WALLS action with label lw calculates the following quantities:
 Quantity   
 Description  
lw.bias
the instantaneous value of the bias potential
lw.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint 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=1000 FILEthe name of the file on which to output these quantities=COLVAR