PLUMED-NEST-TEST-SITE

Project ID: plumID:23.019
Source: plm_path_sketchmap/sketch-map/plumed_for_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
c1: 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
The COM action with label c1 calculates somethingc2: 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
The COM action with label c2 calculates somethingdist1: 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
The DISTANCE action with label dist1 calculates the following quantities:
 Quantity   
 Description  
dist1.value
the DISTANCE between this pair of atomsPRINTPrint 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

#############
# distances from ligand transition state mimetic group COM to each binding site beta sheet Ca atom
The PRINT action with label  calculates somethingd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,c2
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=2,c2
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,c2
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=4,c2
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=5,c2
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,c2
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd7: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,c2
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomsd8: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=8,c2
The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomsd9: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,c2
The DISTANCE action with label d9 calculates the following quantities:
 Quantity   
 Description  
d9.value
the DISTANCE between this pair of atomsd10: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=10,c2
The DISTANCE action with label d10 calculates the following quantities:
 Quantity   
 Description  
d10.value
the DISTANCE between this pair of atomsd11: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,c2
The DISTANCE action with label d11 calculates the following quantities:
 Quantity   
 Description  
d11.value
the DISTANCE between this pair of atomsd12: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=12,c2
The DISTANCE action with label d12 calculates the following quantities:
 Quantity   
 Description  
d12.value
the DISTANCE between this pair of atomsd13: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=13,c2
The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Description  
d13.value
the DISTANCE between this pair of atomsd14: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=14,c2
The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Description  
d14.value
the DISTANCE between this pair of atomsd15: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,c2
The DISTANCE action with label d15 calculates the following quantities:
 Quantity   
 Description  
d15.value
the DISTANCE between this pair of atomsd16: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,c2
The DISTANCE action with label d16 calculates the following quantities:
 Quantity   
 Description  
d16.value
the DISTANCE between this pair of atomsd17: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,c2
The DISTANCE action with label d17 calculates the following quantities:
 Quantity   
 Description  
d17.value
the DISTANCE between this pair of atomsd18: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=18,c2
The DISTANCE action with label d18 calculates the following quantities:
 Quantity   
 Description  
d18.value
the DISTANCE between this pair of atomsd19: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=19,c2
The DISTANCE action with label d19 calculates the following quantities:
 Quantity   
 Description  
d19.value
the DISTANCE between this pair of atomsd20: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=20,c2
The DISTANCE action with label d20 calculates the following quantities:
 Quantity   
 Description  
d20.value
the DISTANCE between this pair of atomsd21: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=21,c2
The DISTANCE action with label d21 calculates the following quantities:
 Quantity   
 Description  
d21.value
the DISTANCE between this pair of atomsd22: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=22,c2
The DISTANCE action with label d22 calculates the following quantities:
 Quantity   
 Description  
d22.value
the DISTANCE between this pair of atomsd23: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=23,c2
The DISTANCE action with label d23 calculates the following quantities:
 Quantity   
 Description  
d23.value
the DISTANCE between this pair of atomsd24: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=24,c2
The DISTANCE action with label d24 calculates the following quantities:
 Quantity   
 Description  
d24.value
the DISTANCE between this pair of atomsd25: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=25,c2
The DISTANCE action with label d25 calculates the following quantities:
 Quantity   
 Description  
d25.value
the DISTANCE between this pair of atomsd26: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=26,c2
The DISTANCE action with label d26 calculates the following quantities:
 Quantity   
 Description  
d26.value
the DISTANCE between this pair of atomsd27: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=27,c2
The DISTANCE action with label d27 calculates the following quantities:
 Quantity   
 Description  
d27.value
the DISTANCE between this pair of atomsd28: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=28,c2
The DISTANCE action with label d28 calculates the following quantities:
 Quantity   
 Description  
d28.value
the DISTANCE between this pair of atomsd29: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=29,c2
The DISTANCE action with label d29 calculates the following quantities:
 Quantity   
 Description  
d29.value
the DISTANCE between this pair of atomsd30: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=30,c2
The DISTANCE action with label d30 calculates the following quantities:
 Quantity   
 Description  
d30.value
the DISTANCE between this pair of atomsd31: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=31,c2
The DISTANCE action with label d31 calculates the following quantities:
 Quantity   
 Description  
d31.value
the DISTANCE between this pair of atomsd32: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=32,c2
The DISTANCE action with label d32 calculates the following quantities:
 Quantity   
 Description  
d32.value
the DISTANCE between this pair of atomsd33: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=33,c2
The DISTANCE action with label d33 calculates the following quantities:
 Quantity   
 Description  
d33.value
the DISTANCE between this pair of atomsd34: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=34,c2
The DISTANCE action with label d34 calculates the following quantities:
 Quantity   
 Description  
d34.value
the DISTANCE between this pair of atomsd35: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=35,c2
The DISTANCE action with label d35 calculates the following quantities:
 Quantity   
 Description  
d35.value
the DISTANCE between this pair of atomsd36: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=36,c2
The DISTANCE action with label d36 calculates the following quantities:
 Quantity   
 Description  
d36.value
the DISTANCE between this pair of atomsd37: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=37,c2
The DISTANCE action with label d37 calculates the following quantities:
 Quantity   
 Description  
d37.value
the DISTANCE between this pair of atomsd38: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=38,c2
The DISTANCE action with label d38 calculates the following quantities:
 Quantity   
 Description  
d38.value
the DISTANCE between this pair of atomsd39: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=39,c2
The DISTANCE action with label d39 calculates the following quantities:
 Quantity   
 Description  
d39.value
the DISTANCE between this pair of atomsd40: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=40,c2
The DISTANCE action with label d40 calculates the following quantities:
 Quantity   
 Description  
d40.value
the DISTANCE between this pair of atomsd41: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=41,c2
The DISTANCE action with label d41 calculates the following quantities:
 Quantity   
 Description  
d41.value
the DISTANCE between this pair of atomsd42: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=42,c2
The DISTANCE action with label d42 calculates the following quantities:
 Quantity   
 Description  
d42.value
the DISTANCE between this pair of atomsd43: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=43,c2
The DISTANCE action with label d43 calculates the following quantities:
 Quantity   
 Description  
d43.value
the DISTANCE between this pair of atomsd44: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=44,c2
The DISTANCE action with label d44 calculates the following quantities:
 Quantity   
 Description  
d44.value
the DISTANCE between this pair of atomsd45: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,c2
The DISTANCE action with label d45 calculates the following quantities:
 Quantity   
 Description  
d45.value
the DISTANCE between this pair of atomsd46: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=46,c2
The DISTANCE action with label d46 calculates the following quantities:
 Quantity   
 Description  
d46.value
the DISTANCE between this pair of atomsd47: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=47,c2
The DISTANCE action with label d47 calculates the following quantities:
 Quantity   
 Description  
d47.value
the DISTANCE between this pair of atomsd48: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=48,c2
The DISTANCE action with label d48 calculates the following quantities:
 Quantity   
 Description  
d48.value
the DISTANCE between this pair of atomsd49: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=49,c2
The DISTANCE action with label d49 calculates the following quantities:
 Quantity   
 Description  
d49.value
the DISTANCE between this pair of atomsd50: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=50,c2
The DISTANCE action with label d50 calculates the following quantities:
 Quantity   
 Description  
d50.value
the DISTANCE between this pair of atomsd51: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=51,c2

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

# Collect distances
The DISTANCE action with label d51 calculates the following quantities:
 Quantity   
 Description  
d51.value
the DISTANCE between this pair of atomsa: COLLECT_FRAMESCollect atomic positions or argument values from the trajectory for later analysis More details ARGthe labels of the values whose time series you would like to collect for later analysis=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

# Make a matrix from the data
The COLLECT_FRAMES action with label a calculates the following quantities:
 Quantity   
 Description  
a.data
the data that is being collected by this action
a.logweights
the logarithms of the weights of the data pointsmat: VSTACKCreate a matrix by stacking vectors together More details ...
    ARG1=a.d1 ARG2=a.d2 ARG3=a.d3 ARG4=a.d4 ARG5=a.d5
    ARG6=a.d6 ARG7=a.d7 ARG8=a.d8 ARG9=a.d9 ARG10=a.d10
    ARG11=a.d11 ARG12=a.d12 ARG13=a.d13 ARG14=a.d14 ARG15=a.d15
    ARG16=a.d16 ARG17=a.d17 ARG18=a.d18 ARG19=a.d19 ARG20=a.d20
    ARG21=a.d21 ARG22=a.d22 ARG23=a.d23 ARG24=a.d24 ARG25=a.d25
    ARG26=a.d26 ARG27=a.d27 ARG28=a.d28 ARG29=a.d29 ARG30=a.d30
    ARG31=a.d31 ARG32=a.d32 ARG33=a.d33 ARG34=a.d34 ARG35=a.d35
    ARG36=a.d36 ARG37=a.d37 ARG38=a.d38 ARG39=a.d39 ARG40=a.d40
    ARG41=a.d41 ARG42=a.d42 ARG43=a.d43 ARG44=a.d44 ARG45=a.d45
    ARG46=a.d46 ARG47=a.d47 ARG48=a.d48 ARG49=a.d49 ARG50=a.d50
    ARG51=a.d51
...

# Transpose the data matrix
The VSTACK action with label mat calculates the following quantities:
 Quantity   
 Description  
mat.value
a matrix that contains the input vectors in its columnsmatT: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=mat

# Now calculate the dissimilarities 
The TRANSPOSE action with label matT calculates the following quantities:
 Quantity   
 Description  
matT.value
the transpose of the input matrixdistmat: DISSIMILARITIESCalculate the matrix of dissimilarities between a trajectory of atomic configurations. More details SQUARED calculate the squares of the dissimilarities (this option cannot be used with MATRIX_PRODUCT) ARG1=mat ARG2=matT

# Select landmarks
The DISSIMILARITIES action with label distmat calculates the following quantities:
 Quantity   
 Description  
distmat.value
the product of the two input matricesfps: LANDMARK_SELECT_FPSSelect a of landmarks from a large set of configurations using farthest point sampling. More details ...
    ARG1=a.d1 ARG2=a.d2 ARG3=a.d3 ARG4=a.d4 ARG5=a.d5
    ARG6=a.d6 ARG7=a.d7 ARG8=a.d8 ARG9=a.d9 ARG10=a.d10
    ARG11=a.d11 ARG12=a.d12 ARG13=a.d13 ARG14=a.d14 ARG15=a.d15
    ARG16=a.d16 ARG17=a.d17 ARG18=a.d18 ARG19=a.d19 ARG20=a.d20
    ARG21=a.d21 ARG22=a.d22 ARG23=a.d23 ARG24=a.d24 ARG25=a.d25
    ARG26=a.d26 ARG27=a.d27 ARG28=a.d28 ARG29=a.d29 ARG30=a.d30
    ARG31=a.d31 ARG32=a.d32 ARG33=a.d33 ARG34=a.d34 ARG35=a.d35
    ARG36=a.d36 ARG37=a.d37 ARG38=a.d38 ARG39=a.d39 ARG40=a.d40
    ARG41=a.d41 ARG42=a.d42 ARG43=a.d43 ARG44=a.d44 ARG45=a.d45
    ARG46=a.d46 ARG47=a.d47 ARG48=a.d48 ARG49=a.d49 ARG50=a.d50
    ARG51=a.d51 ARG52=distmat NLANDMARKSthe numbe rof landmarks you would like to create=50
...

# Do a voronoi analysis to work out the closet point to each landmark
The LANDMARK_SELECT_FPS action with label fps calculates the following quantities:
 Quantity   
 Description  voro: VORONOIDo a voronoi analysis More details ARGthe distance/adjacency matrix that should be used to perform the voronoi analysis=fps.distmat_rect

# Take the exponential of the log weights
The VORONOI action with label voro calculates the following quantities:
 Quantity   
 Description  
voro.value
a matrix in which element ij is equal to one if the ij component of the input matrix is lower than all the ik elements of the matrix where k is not j and zero otherwiseweights: CUSTOMCalculate a combination of variables using a custom expression. More details ARG1=a.logweights FUNCthe function you wish to evaluate=exp(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Now calculate the weight of each point by multiplying the voronoi matrix by the vector of weights
The CUSTOM action with label weights calculates the following quantities:
 Quantity   
 Description  
weights.value
an arbitrary functionlwe: DOTThis action is not part of PLUMED and was included by using a LOAD command More details ARG1=voro ARG2=weights

# Run Sketch map
smap: SKETCHMAPConstruct a sketch map projection of the input data More details ...
    DISSIMILARITIES=fps.distmat_sqr
    NLOW_DIMnumber of low-dimensional coordinates required=2
    WEIGHTSa vector containing the weights of the points=lwe
    HIGH_DIM_FUNCTIONthe parameters of the switching function in the high dimensional space={SMAP R_0=1 A=2 B=2}
    LOW_DIM_FUNCTIONthe parameters of the switching function in the low dimensional space={SMAP R_0=1 A=2 B=2}
    CGTOL The tolerance for the conjugate gradient minimization that finds the projection of the landmarks=1E1
    CGRID_SIZE number of points to use in each grid direction=20,20
    FGRID_SIZE interpolate the grid onto this number of points -- only works in 2D=200,200
    NCYCLES The number of cycles of pointwise global optimisation that are required=5
...

The SKETCHMAP action with label smap calculates the following quantities:
 Quantity   
 Description  
smap.value
the sketch-map projection of the input pointsoutput1: 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=reference_data.dat
The PRINT action with label output1 calculates somethingoutput2: 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,fps.*,lwe FILEthe name of the file on which to output these quantities=reference_data.pdb
The PRINT action with label output2 calculates something