PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:23.019
Source: plm_path_sketchmap/sketch-map/plumed_map_to_reference_map.dat
Originally used with PLUMED version: 2.7.2
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
# ligand transition state mimetic and catalytic site COMs
c1The COM action with label c1 calculates the following quantities: Quantity    Type    Description  
c1 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=7,51 #a spartic dyad ASH80CG, ASP313CG
c2The COM action with label c2 calculates the following quantities: Quantity    Type    Description  
c2 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=52,53 # ligand transition state mimetic atoms

# calculate and output distance between the ligand transition state mimetic and catalytic site
dist1The DISTANCE action with label dist1 calculates the following quantities: Quantity    Type    Description  
dist1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=c1,c2 #distance between catalytic site and ligand COM
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dist1 FILEthe name of the file on which to output these quantities=dist1.dat

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# distances from ligand transition state mimetic group COM to each binding site beta sheet Ca atom
The PRINT action with label  calculates somethingd1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,c2
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,c2
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,c2
d4The DISTANCE action with label d4 calculates the following quantities: Quantity    Type    Description  
d4 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,c2
d5The DISTANCE action with label d5 calculates the following quantities: Quantity    Type    Description  
d5 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,c2
d6The DISTANCE action with label d6 calculates the following quantities: Quantity    Type    Description  
d6 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,c2
d7The DISTANCE action with label d7 calculates the following quantities: Quantity    Type    Description  
d7 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,c2
d8The DISTANCE action with label d8 calculates the following quantities: Quantity    Type    Description  
d8 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=8,c2
d9The DISTANCE action with label d9 calculates the following quantities: Quantity    Type    Description  
d9 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,c2
d10The DISTANCE action with label d10 calculates the following quantities: Quantity    Type    Description  
d10 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,c2
d11The DISTANCE action with label d11 calculates the following quantities: Quantity    Type    Description  
d11 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,c2
d12The DISTANCE action with label d12 calculates the following quantities: Quantity    Type    Description  
d12 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=12,c2
d13The DISTANCE action with label d13 calculates the following quantities: Quantity    Type    Description  
d13 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=13,c2
d14The DISTANCE action with label d14 calculates the following quantities: Quantity    Type    Description  
d14 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=14,c2
d15The DISTANCE action with label d15 calculates the following quantities: Quantity    Type    Description  
d15 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,c2
d16The DISTANCE action with label d16 calculates the following quantities: Quantity    Type    Description  
d16 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,c2
d17The DISTANCE action with label d17 calculates the following quantities: Quantity    Type    Description  
d17 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,c2
d18The DISTANCE action with label d18 calculates the following quantities: Quantity    Type    Description  
d18 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=18,c2
d19The DISTANCE action with label d19 calculates the following quantities: Quantity    Type    Description  
d19 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=19,c2
d20The DISTANCE action with label d20 calculates the following quantities: Quantity    Type    Description  
d20 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=20,c2
d21The DISTANCE action with label d21 calculates the following quantities: Quantity    Type    Description  
d21 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=21,c2
d22The DISTANCE action with label d22 calculates the following quantities: Quantity    Type    Description  
d22 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=22,c2
d23The DISTANCE action with label d23 calculates the following quantities: Quantity    Type    Description  
d23 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=23,c2
d24The DISTANCE action with label d24 calculates the following quantities: Quantity    Type    Description  
d24 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=24,c2
d25The DISTANCE action with label d25 calculates the following quantities: Quantity    Type    Description  
d25 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,c2
d26The DISTANCE action with label d26 calculates the following quantities: Quantity    Type    Description  
d26 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,c2
d27The DISTANCE action with label d27 calculates the following quantities: Quantity    Type    Description  
d27 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=27,c2
d28The DISTANCE action with label d28 calculates the following quantities: Quantity    Type    Description  
d28 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=28,c2
d29The DISTANCE action with label d29 calculates the following quantities: Quantity    Type    Description  
d29 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=29,c2
d30The DISTANCE action with label d30 calculates the following quantities: Quantity    Type    Description  
d30 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=30,c2
d31The DISTANCE action with label d31 calculates the following quantities: Quantity    Type    Description  
d31 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=31,c2
d32The DISTANCE action with label d32 calculates the following quantities: Quantity    Type    Description  
d32 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=32,c2
d33The DISTANCE action with label d33 calculates the following quantities: Quantity    Type    Description  
d33 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=33,c2
d34The DISTANCE action with label d34 calculates the following quantities: Quantity    Type    Description  
d34 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=34,c2
d35The DISTANCE action with label d35 calculates the following quantities: Quantity    Type    Description  
d35 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=35,c2
d36The DISTANCE action with label d36 calculates the following quantities: Quantity    Type    Description  
d36 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=36,c2
d37The DISTANCE action with label d37 calculates the following quantities: Quantity    Type    Description  
d37 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=37,c2
d38The DISTANCE action with label d38 calculates the following quantities: Quantity    Type    Description  
d38 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=38,c2
d39The DISTANCE action with label d39 calculates the following quantities: Quantity    Type    Description  
d39 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=39,c2
d40The DISTANCE action with label d40 calculates the following quantities: Quantity    Type    Description  
d40 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=40,c2
d41The DISTANCE action with label d41 calculates the following quantities: Quantity    Type    Description  
d41 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=41,c2
d42The DISTANCE action with label d42 calculates the following quantities: Quantity    Type    Description  
d42 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=42,c2
d43The DISTANCE action with label d43 calculates the following quantities: Quantity    Type    Description  
d43 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=43,c2
d44The DISTANCE action with label d44 calculates the following quantities: Quantity    Type    Description  
d44 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=44,c2
d45The DISTANCE action with label d45 calculates the following quantities: Quantity    Type    Description  
d45 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,c2
d46The DISTANCE action with label d46 calculates the following quantities: Quantity    Type    Description  
d46 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=46,c2
d47The DISTANCE action with label d47 calculates the following quantities: Quantity    Type    Description  
d47 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,c2
d48The DISTANCE action with label d48 calculates the following quantities: Quantity    Type    Description  
d48 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=48,c2
d49The DISTANCE action with label d49 calculates the following quantities: Quantity    Type    Description  
d49 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=49,c2
d50The DISTANCE action with label d50 calculates the following quantities: Quantity    Type    Description  
d50 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=50,c2
d51The DISTANCE action with label d51 calculates the following quantities: Quantity    Type    Description  
d51 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=51,c2

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smapThe PROJECT_POINTS action with label smap calculates the following quantities: Quantity    Type    Description  
smap.coord-1 scalar the coordinates of the points in the low dimensional space  This is the 1th of these quantities
smap.coord-2 scalar the coordinates of the points in the low dimensional space  This is the 2th of these quantities: SKETCHMAP_PROJECTIONRead in a sketch-map projection This action is a shortcut and it has hidden defaults. More details ...
    ARGthe list of arguments you would like to use in your definition of the path=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45,d46,d47,d48,d49,d50,d51
    REFERENCEa pdb file containing the set of reference configurations=ref_data.pdb # reference sketchmap that was previously created 
    PROPERTYthe property to be used in the index=smap_coord-1,smap_coord-2
    WEIGHTthe weight of each individual landmark in the stress fucntion that is to be optimised=lwe
    HIGH_DIM_FUNCTIONthe parameters of the switching function in the high dimensional space={SMAP R_0=1.5 A=2 B=2}
    LOW_DIM_FUNCTIONthe parameters of the switching function in the low dimensional space={SMAP R_0=1.5 A=2 B=2}
    CGTOL The tolerance for the conjugate gradient minimization that finds the out of sample projections=1E-3
... 
smap: SKETCHMAP_PROJECTIONRead in a sketch-map projection This action is a shortcut and uses the defaults shown here. More details ...
    ARGthe list of arguments you would like to use in your definition of the path=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45,d46,d47,d48,d49,d50,d51
    REFERENCEa pdb file containing the set of reference configurations=ref_data.pdb # reference sketchmap that was previously created 
    PROPERTYthe property to be used in the index=smap_coord-1,smap_coord-2
    WEIGHTthe weight of each individual landmark in the stress fucntion that is to be optimised=lwe
    HIGH_DIM_FUNCTIONthe parameters of the switching function in the high dimensional space={SMAP R_0=1.5 A=2 B=2}
    LOW_DIM_FUNCTIONthe parameters of the switching function in the low dimensional space={SMAP R_0=1.5 A=2 B=2}
    CGTOL The tolerance for the conjugate gradient minimization that finds the out of sample projections=1E-3
 TYPE the manner in which distances are calculated=OPTIMAL-FAST
... 
# PLUMED interprets the command:
# smap: SKETCHMAP_PROJECTION ...
#     ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45,d46,d47,d48,d49,d50,d51
#     REFERENCE=ref_data.pdb # reference sketchmap that was previously created 
#     PROPERTY=smap_coord-1,smap_coord-2
#     WEIGHT=lwe
#     HIGH_DIM_FUNCTION={SMAP R_0=1.5 A=2 B=2}
#     LOW_DIM_FUNCTION={SMAP R_0=1.5 A=2 B=2}
#     CGTOL=1E-3
# ... 
# as follows (Click the red comment above to revert to the short version of the input):
smap_ref_d1The CONSTANT action with label smap_ref_d1 calculates the following quantities: Quantity    Type    Description  
smap_ref_d1 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d1
smap_ref_d2The CONSTANT action with label smap_ref_d2 calculates the following quantities: Quantity    Type    Description  
smap_ref_d2 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d2
smap_ref_d3The CONSTANT action with label smap_ref_d3 calculates the following quantities: Quantity    Type    Description  
smap_ref_d3 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d3
smap_ref_d4The CONSTANT action with label smap_ref_d4 calculates the following quantities: Quantity    Type    Description  
smap_ref_d4 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d4
smap_ref_d5The CONSTANT action with label smap_ref_d5 calculates the following quantities: Quantity    Type    Description  
smap_ref_d5 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d5
smap_ref_d6The CONSTANT action with label smap_ref_d6 calculates the following quantities: Quantity    Type    Description  
smap_ref_d6 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d6
smap_ref_d7The CONSTANT action with label smap_ref_d7 calculates the following quantities: Quantity    Type    Description  
smap_ref_d7 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d7
smap_ref_d8The CONSTANT action with label smap_ref_d8 calculates the following quantities: Quantity    Type    Description  
smap_ref_d8 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d8
smap_ref_d9The CONSTANT action with label smap_ref_d9 calculates the following quantities: Quantity    Type    Description  
smap_ref_d9 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d9
smap_ref_d10The CONSTANT action with label smap_ref_d10 calculates the following quantities: Quantity    Type    Description  
smap_ref_d10 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d10
smap_ref_d11The CONSTANT action with label smap_ref_d11 calculates the following quantities: Quantity    Type    Description  
smap_ref_d11 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d11
smap_ref_d12The CONSTANT action with label smap_ref_d12 calculates the following quantities: Quantity    Type    Description  
smap_ref_d12 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d12
smap_ref_d13The CONSTANT action with label smap_ref_d13 calculates the following quantities: Quantity    Type    Description  
smap_ref_d13 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d13
smap_ref_d14The CONSTANT action with label smap_ref_d14 calculates the following quantities: Quantity    Type    Description  
smap_ref_d14 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d14
smap_ref_d15The CONSTANT action with label smap_ref_d15 calculates the following quantities: Quantity    Type    Description  
smap_ref_d15 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d15
smap_ref_d16The CONSTANT action with label smap_ref_d16 calculates the following quantities: Quantity    Type    Description  
smap_ref_d16 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d16
smap_ref_d17The CONSTANT action with label smap_ref_d17 calculates the following quantities: Quantity    Type    Description  
smap_ref_d17 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d17
smap_ref_d18The CONSTANT action with label smap_ref_d18 calculates the following quantities: Quantity    Type    Description  
smap_ref_d18 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d18
smap_ref_d19The CONSTANT action with label smap_ref_d19 calculates the following quantities: Quantity    Type    Description  
smap_ref_d19 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d19
smap_ref_d20The CONSTANT action with label smap_ref_d20 calculates the following quantities: Quantity    Type    Description  
smap_ref_d20 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d20
smap_ref_d21The CONSTANT action with label smap_ref_d21 calculates the following quantities: Quantity    Type    Description  
smap_ref_d21 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d21
smap_ref_d22The CONSTANT action with label smap_ref_d22 calculates the following quantities: Quantity    Type    Description  
smap_ref_d22 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d22
smap_ref_d23The CONSTANT action with label smap_ref_d23 calculates the following quantities: Quantity    Type    Description  
smap_ref_d23 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d23
smap_ref_d24The CONSTANT action with label smap_ref_d24 calculates the following quantities: Quantity    Type    Description  
smap_ref_d24 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d24
smap_ref_d25The CONSTANT action with label smap_ref_d25 calculates the following quantities: Quantity    Type    Description  
smap_ref_d25 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d25
smap_ref_d26The CONSTANT action with label smap_ref_d26 calculates the following quantities: Quantity    Type    Description  
smap_ref_d26 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d26
smap_ref_d27The CONSTANT action with label smap_ref_d27 calculates the following quantities: Quantity    Type    Description  
smap_ref_d27 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d27
smap_ref_d28The CONSTANT action with label smap_ref_d28 calculates the following quantities: Quantity    Type    Description  
smap_ref_d28 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d28
smap_ref_d29The CONSTANT action with label smap_ref_d29 calculates the following quantities: Quantity    Type    Description  
smap_ref_d29 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d29
smap_ref_d30The CONSTANT action with label smap_ref_d30 calculates the following quantities: Quantity    Type    Description  
smap_ref_d30 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d30
smap_ref_d31The CONSTANT action with label smap_ref_d31 calculates the following quantities: Quantity    Type    Description  
smap_ref_d31 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d31
smap_ref_d32The CONSTANT action with label smap_ref_d32 calculates the following quantities: Quantity    Type    Description  
smap_ref_d32 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d32
smap_ref_d33The CONSTANT action with label smap_ref_d33 calculates the following quantities: Quantity    Type    Description  
smap_ref_d33 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d33
smap_ref_d34The CONSTANT action with label smap_ref_d34 calculates the following quantities: Quantity    Type    Description  
smap_ref_d34 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d34
smap_ref_d35The CONSTANT action with label smap_ref_d35 calculates the following quantities: Quantity    Type    Description  
smap_ref_d35 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d35
smap_ref_d36The CONSTANT action with label smap_ref_d36 calculates the following quantities: Quantity    Type    Description  
smap_ref_d36 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d36
smap_ref_d37The CONSTANT action with label smap_ref_d37 calculates the following quantities: Quantity    Type    Description  
smap_ref_d37 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d37
smap_ref_d38The CONSTANT action with label smap_ref_d38 calculates the following quantities: Quantity    Type    Description  
smap_ref_d38 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d38
smap_ref_d39The CONSTANT action with label smap_ref_d39 calculates the following quantities: Quantity    Type    Description  
smap_ref_d39 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d39
smap_ref_d40The CONSTANT action with label smap_ref_d40 calculates the following quantities: Quantity    Type    Description  
smap_ref_d40 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d40
smap_ref_d41The CONSTANT action with label smap_ref_d41 calculates the following quantities: Quantity    Type    Description  
smap_ref_d41 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d41
smap_ref_d42The CONSTANT action with label smap_ref_d42 calculates the following quantities: Quantity    Type    Description  
smap_ref_d42 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d42
smap_ref_d43The CONSTANT action with label smap_ref_d43 calculates the following quantities: Quantity    Type    Description  
smap_ref_d43 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d43
smap_ref_d44The CONSTANT action with label smap_ref_d44 calculates the following quantities: Quantity    Type    Description  
smap_ref_d44 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d44
smap_ref_d45The CONSTANT action with label smap_ref_d45 calculates the following quantities: Quantity    Type    Description  
smap_ref_d45 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d45
smap_ref_d46The CONSTANT action with label smap_ref_d46 calculates the following quantities: Quantity    Type    Description  
smap_ref_d46 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d46
smap_ref_d47The CONSTANT action with label smap_ref_d47 calculates the following quantities: Quantity    Type    Description  
smap_ref_d47 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d47
smap_ref_d48The CONSTANT action with label smap_ref_d48 calculates the following quantities: Quantity    Type    Description  
smap_ref_d48 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d48
smap_ref_d49The CONSTANT action with label smap_ref_d49 calculates the following quantities: Quantity    Type    Description  
smap_ref_d49 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d49
smap_ref_d50The CONSTANT action with label smap_ref_d50 calculates the following quantities: Quantity    Type    Description  
smap_ref_d50 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d50
smap_ref_d51The CONSTANT action with label smap_ref_d51 calculates the following quantities: Quantity    Type    Description  
smap_ref_d51 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=d51
smap_dataThe MATRIX_PRODUCT_DIAGONAL action with label smap_data calculates the following quantities: Quantity    Type    Description  
smap_data vector a vector containing the diagonal elements of the matrix that obtaned by multiplying the two input matrices together: EUCLIDEAN_DISTANCECalculate the euclidean distance between two vectors of arguments More details SQUARED The squared distance should be calculated ARG1The poin that we are calculating the distance from=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45,d46,d47,d48,d49,d50,d51 ARG2The point that we are calculating the distance to=smap_ref_d1,smap_ref_d2,smap_ref_d3,smap_ref_d4,smap_ref_d5,smap_ref_d6,smap_ref_d7,smap_ref_d8,smap_ref_d9,smap_ref_d10,smap_ref_d11,smap_ref_d12,smap_ref_d13,smap_ref_d14,smap_ref_d15,smap_ref_d16,smap_ref_d17,smap_ref_d18,smap_ref_d19,smap_ref_d20,smap_ref_d21,smap_ref_d22,smap_ref_d23,smap_ref_d24,smap_ref_d25,smap_ref_d26,smap_ref_d27,smap_ref_d28,smap_ref_d29,smap_ref_d30,smap_ref_d31,smap_ref_d32,smap_ref_d33,smap_ref_d34,smap_ref_d35,smap_ref_d36,smap_ref_d37,smap_ref_d38,smap_ref_d39,smap_ref_d40,smap_ref_d41,smap_ref_d42,smap_ref_d43,smap_ref_d44,smap_ref_d45,smap_ref_d46,smap_ref_d47,smap_ref_d48,smap_ref_d49,smap_ref_d50,smap_ref_d51
smap_coord-1The CONSTANT action with label smap_coord-1 calculates the following quantities: Quantity    Type    Description  
smap_coord-1 scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
smap_coord-1_refThe CONSTANT action with label smap_coord-1_ref calculates the following quantities: Quantity    Type    Description  
smap_coord-1_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=smap_coord-1
smap_coord-2The CONSTANT action with label smap_coord-2 calculates the following quantities: Quantity    Type    Description  
smap_coord-2 scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
smap_coord-2_refThe CONSTANT action with label smap_coord-2_ref calculates the following quantities: Quantity    Type    Description  
smap_coord-2_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=smap_coord-2
lweThe CONSTANT action with label lwe calculates the following quantities: Quantity    Type    Description  
lwe scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
lwe_refThe CONSTANT action with label lwe_ref calculates the following quantities: Quantity    Type    Description  
lwe_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=ref_data.pdb ARGread this single argument from the input rather than the atomic structure=lwe
smap_wsumThe SUM action with label smap_wsum calculates the following quantities: Quantity    Type    Description  
smap_wsum scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe values input to this function=lwe_ref
smap_weightsThe CUSTOM action with label smap_weights calculates the following quantities: Quantity    Type    Description  
smap_weights vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=smap_wsum,lwe_ref FUNCthe function you wish to evaluate=y/x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
smap_targThe MORE_THAN action with label smap_targ calculates the following quantities: Quantity    Type    Description  
smap_targ vector the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=smap_data SQUARED is the input quantity the square of the value that you would like to apply the switching function to SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=1.5 A=2 B=2}
smap: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input More details ARGthe projections of the landmark points=smap_coord-1_ref,smap_coord-2_ref TARGET1the matrix of target quantities that you would like to match=smap_targ FUNC1a function that is applied on the distances between the points in the low dimensional space={SMAP R_0=1.5 A=2 B=2} WEIGHTS1the matrix with the weights of the target quantities=smap_weights CGTOL the tolerance for the conjugate gradient minimization=1E-3
# --- End of included input --- 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=smap.coord-1,smap.coord-2 FILEthe name of the file on which to output these quantities=smap_data.dat
Quantity	Type	Description
c1	atoms	virtual atom calculated by COM action
PLUMED-NEST-TEST-SITE

The public repository of the PLUMED consortium
