Project ID: plumID:23.019
Source: plm_path_sketchmap/sketch-map/plumed_sketchmap.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
tested onv2.9
tested onmaster
# ligand transition state mimetic and catalytic site COMs
c1: 
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the list of atoms which are involved the virtual atom's definition
=7,51 #a spartic dyad ASH80CG, ASP313CG c2:
COM
Calculate the center of mass for a group of atoms. More details
ATOMS
the 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 dist1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=c1,c2 #distance between catalytic site and ligand COM
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=dist1
FILE
the 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 d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=1,c2 d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2,c2 d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=3,c2 d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=4,c2 d5:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=5,c2 d6:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=6,c2 d7:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=7,c2 d8:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=8,c2 d9:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=9,c2 d10:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=10,c2 d11:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=11,c2 d12:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=12,c2 d13:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=13,c2 d14:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=14,c2 d15:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=15,c2 d16:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=16,c2 d17:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=17,c2 d18:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=18,c2 d19:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=19,c2 d20:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=20,c2 d21:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=21,c2 d22:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=22,c2 d23:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=23,c2 d24:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=24,c2 d25:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=25,c2 d26:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=26,c2 d27:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=27,c2 d28:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=28,c2 d29:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=29,c2 d30:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=30,c2 d31:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=31,c2 d32:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=32,c2 d33:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=33,c2 d34:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=34,c2 d35:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=35,c2 d36:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=36,c2 d37:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=37,c2 d38:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=38,c2 d39:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=39,c2 d40:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=40,c2 d41:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=41,c2 d42:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=42,c2 d43:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=43,c2 d44:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=44,c2 d45:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=45,c2 d46:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=46,c2 d47:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=47,c2 d48:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=48,c2 d49:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=49,c2 d50:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=50,c2 d51:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=51,c2
###################
# Collect distances a:
COLLECT_FRAMES
This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object More details
ARG
the input for this action is the scalar output from one or more other actions
=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 mat:
VSTACK
Create a matrix by stacking vectors together More details
...
ARG1
the input for this action is the scalar output from one or more other actions
=a.d1
ARG2
the input for this action is the scalar output from one or more other actions
=a.d2
ARG3
the input for this action is the scalar output from one or more other actions
=a.d3
ARG4
the input for this action is the scalar output from one or more other actions
=a.d4
ARG5
the input for this action is the scalar output from one or more other actions
=a.d5
ARG6
the input for this action is the scalar output from one or more other actions
=a.d6
ARG7
the input for this action is the scalar output from one or more other actions
=a.d7
ARG8
the input for this action is the scalar output from one or more other actions
=a.d8
ARG9
the input for this action is the scalar output from one or more other actions
=a.d9
ARG10
the input for this action is the scalar output from one or more other actions
=a.d10
ARG11
the input for this action is the scalar output from one or more other actions
=a.d11
ARG12
the input for this action is the scalar output from one or more other actions
=a.d12
ARG13
the input for this action is the scalar output from one or more other actions
=a.d13
ARG14
the input for this action is the scalar output from one or more other actions
=a.d14
ARG15
the input for this action is the scalar output from one or more other actions
=a.d15
ARG16
the input for this action is the scalar output from one or more other actions
=a.d16
ARG17
the input for this action is the scalar output from one or more other actions
=a.d17
ARG18
the input for this action is the scalar output from one or more other actions
=a.d18
ARG19
the input for this action is the scalar output from one or more other actions
=a.d19
ARG20
the input for this action is the scalar output from one or more other actions
=a.d20
ARG21
the input for this action is the scalar output from one or more other actions
=a.d21
ARG22
the input for this action is the scalar output from one or more other actions
=a.d22
ARG23
the input for this action is the scalar output from one or more other actions
=a.d23
ARG24
the input for this action is the scalar output from one or more other actions
=a.d24
ARG25
the input for this action is the scalar output from one or more other actions
=a.d25
ARG26
the input for this action is the scalar output from one or more other actions
=a.d26
ARG27
the input for this action is the scalar output from one or more other actions
=a.d27
ARG28
the input for this action is the scalar output from one or more other actions
=a.d28
ARG29
the input for this action is the scalar output from one or more other actions
=a.d29
ARG30
the input for this action is the scalar output from one or more other actions
=a.d30
ARG31
the input for this action is the scalar output from one or more other actions
=a.d31
ARG32
the input for this action is the scalar output from one or more other actions
=a.d32
ARG33
the input for this action is the scalar output from one or more other actions
=a.d33
ARG34
the input for this action is the scalar output from one or more other actions
=a.d34
ARG35
the input for this action is the scalar output from one or more other actions
=a.d35
ARG36
the input for this action is the scalar output from one or more other actions
=a.d36
ARG37
the input for this action is the scalar output from one or more other actions
=a.d37
ARG38
the input for this action is the scalar output from one or more other actions
=a.d38
ARG39
the input for this action is the scalar output from one or more other actions
=a.d39
ARG40
the input for this action is the scalar output from one or more other actions
=a.d40
ARG41
the input for this action is the scalar output from one or more other actions
=a.d41
ARG42
the input for this action is the scalar output from one or more other actions
=a.d42
ARG43
the input for this action is the scalar output from one or more other actions
=a.d43
ARG44
the input for this action is the scalar output from one or more other actions
=a.d44
ARG45
the input for this action is the scalar output from one or more other actions
=a.d45
ARG46
the input for this action is the scalar output from one or more other actions
=a.d46
ARG47
the input for this action is the scalar output from one or more other actions
=a.d47
ARG48
the input for this action is the scalar output from one or more other actions
=a.d48
ARG49
the input for this action is the scalar output from one or more other actions
=a.d49
ARG50
the input for this action is the scalar output from one or more other actions
=a.d50
ARG51
the input for this action is the scalar output from one or more other actions
=a.d51 ...
# Transpose the data matrix matT:
TRANSPOSE
Calculate the transpose of a matrix More details
ARG
the input for this action is the scalar output from one or more other actions
=mat
# Now calculate the dissimilarities distmat:
DISSIMILARITIES
This action is not part of PLUMED and was included by using a LOAD command More details
SQUARED ARG1=mat ARG2=matT
# Select landmarks fps:
LANDMARK_SELECT_FPS
Select a set of landmarks 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
NLANDMARKS
the number of landmarks that you would like to select
=50 ...
# Do a voronoi analysis to work out the closet point to each landmark voro:
VORONOI
This action is not part of PLUMED and was included by using a LOAD command More details
ARG=fps.distmat_rect
# Take the exponential of the log weights weights:
CUSTOM
Calculate a combination of variables using a custom expression. More details
ARG1
the input to this function
=a.logweights
FUNC
the function you wish to evaluate
=exp(x
PERIODIC
if 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 lwe:
DOT
This action is not part of PLUMED and was included by using a LOAD command More details
ARG1=voro ARG2=weights
# Run Sketch map smap:
SKETCHMAP
This action is not part of PLUMED and was included by using a LOAD command More details
... DISSIMILARITIES=fps.distmat_sqr NLOW_DIM=2 WEIGHTS=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=1E1 OS_CGTOL=1E1 CGRID_SIZE=20,20 FGRID_SIZE=200,200 NCYCLES=5 PROJECT_ALL ...
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=smap_osample.coord-1,smap_osample.coord-2
FILE
the name of the file on which to output these quantities
=smap_data.dat