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
# ligand transition state mimetic and catalytic site COMs c1:COMCalculate the center of mass for a group of atoms. More detailsATOMS=7,51 #a spartic dyad ASH80CG, ASP313CG c2:the list of atoms which are involved the virtual atom's definitionCOMCalculate the center of mass for a group of atoms. More detailsATOMS=52,53 # ligand transition state mimetic atomsthe list of atoms which are involved the virtual atom's definition
# calculate and output distance between the ligand transition state mimetic and catalytic site dist1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=c1,c2 #distance between catalytic site and ligand COMthe pair of atom that we are calculating the distance betweenPrint quantities to a file. More detailsARG=dist1the input for this action is the scalar output from one or more other actionsFILE=dist1.datthe name of the file on which to output these quantities
############# # distances from ligand transition state mimetic group COM to each binding site beta sheet Ca atom d1:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=1,c2 d2:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=2,c2 d3:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=3,c2 d4:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=4,c2 d5:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=5,c2 d6:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=6,c2 d7:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=7,c2 d8:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=8,c2 d9:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=9,c2 d10:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=10,c2 d11:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=11,c2 d12:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=12,c2 d13:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=13,c2 d14:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=14,c2 d15:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=15,c2 d16:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=16,c2 d17:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=17,c2 d18:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=18,c2 d19:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=19,c2 d20:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=20,c2 d21:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=21,c2 d22:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=22,c2 d23:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=23,c2 d24:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=24,c2 d25:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=25,c2 d26:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=26,c2 d27:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=27,c2 d28:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=28,c2 d29:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=29,c2 d30:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=30,c2 d31:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=31,c2 d32:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=32,c2 d33:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=33,c2 d34:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=34,c2 d35:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=35,c2 d36:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=36,c2 d37:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=37,c2 d38:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=38,c2 d39:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=39,c2 d40:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=40,c2 d41:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=41,c2 d42:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=42,c2 d43:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=43,c2 d44:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=44,c2 d45:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=45,c2 d46:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=46,c2 d47:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=47,c2 d48:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=48,c2 d49:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=49,c2 d50:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=50,c2 d51:the pair of atom that we are calculating the distance betweenDISTANCECalculate the distance between a pair of atoms. More detailsATOMS=51,c2the pair of atom that we are calculating the distance between
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# Collect distances a:COLLECT_FRAMESThis allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object More detailsARG=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,d51the input for this action is the scalar output from one or more other actions
# Make a matrix from the data mat:VSTACK...Create a matrix by stacking vectors together More detailsARG1=a.d1the input for this action is the scalar output from one or more other actionsARG2=a.d2the input for this action is the scalar output from one or more other actionsARG3=a.d3the input for this action is the scalar output from one or more other actionsARG4=a.d4the input for this action is the scalar output from one or more other actionsARG5=a.d5the input for this action is the scalar output from one or more other actionsARG6=a.d6the input for this action is the scalar output from one or more other actionsARG7=a.d7the input for this action is the scalar output from one or more other actionsARG8=a.d8the input for this action is the scalar output from one or more other actionsARG9=a.d9the input for this action is the scalar output from one or more other actionsARG10=a.d10the input for this action is the scalar output from one or more other actionsARG11=a.d11the input for this action is the scalar output from one or more other actionsARG12=a.d12the input for this action is the scalar output from one or more other actionsARG13=a.d13the input for this action is the scalar output from one or more other actionsARG14=a.d14the input for this action is the scalar output from one or more other actionsARG15=a.d15the input for this action is the scalar output from one or more other actionsARG16=a.d16the input for this action is the scalar output from one or more other actionsARG17=a.d17the input for this action is the scalar output from one or more other actionsARG18=a.d18the input for this action is the scalar output from one or more other actionsARG19=a.d19the input for this action is the scalar output from one or more other actionsARG20=a.d20the input for this action is the scalar output from one or more other actionsARG21=a.d21the input for this action is the scalar output from one or more other actionsARG22=a.d22the input for this action is the scalar output from one or more other actionsARG23=a.d23the input for this action is the scalar output from one or more other actionsARG24=a.d24the input for this action is the scalar output from one or more other actionsARG25=a.d25the input for this action is the scalar output from one or more other actionsARG26=a.d26the input for this action is the scalar output from one or more other actionsARG27=a.d27the input for this action is the scalar output from one or more other actionsARG28=a.d28the input for this action is the scalar output from one or more other actionsARG29=a.d29the input for this action is the scalar output from one or more other actionsARG30=a.d30the input for this action is the scalar output from one or more other actionsARG31=a.d31the input for this action is the scalar output from one or more other actionsARG32=a.d32the input for this action is the scalar output from one or more other actionsARG33=a.d33the input for this action is the scalar output from one or more other actionsARG34=a.d34the input for this action is the scalar output from one or more other actionsARG35=a.d35the input for this action is the scalar output from one or more other actionsARG36=a.d36the input for this action is the scalar output from one or more other actionsARG37=a.d37the input for this action is the scalar output from one or more other actionsARG38=a.d38the input for this action is the scalar output from one or more other actionsARG39=a.d39the input for this action is the scalar output from one or more other actionsARG40=a.d40the input for this action is the scalar output from one or more other actionsARG41=a.d41the input for this action is the scalar output from one or more other actionsARG42=a.d42the input for this action is the scalar output from one or more other actionsARG43=a.d43the input for this action is the scalar output from one or more other actionsARG44=a.d44the input for this action is the scalar output from one or more other actionsARG45=a.d45the input for this action is the scalar output from one or more other actionsARG46=a.d46the input for this action is the scalar output from one or more other actionsARG47=a.d47the input for this action is the scalar output from one or more other actionsARG48=a.d48the input for this action is the scalar output from one or more other actionsARG49=a.d49the input for this action is the scalar output from one or more other actionsARG50=a.d50the input for this action is the scalar output from one or more other actionsARG51=a.d51 ...the input for this action is the scalar output from one or more other actions
# Transpose the data matrix matT:TRANSPOSECalculate the transpose of a matrix More detailsARG=matthe input for this action is the scalar output from one or more other actions
# Now calculate the dissimilarities distmat:DISSIMILARITIESSQUARED ARG1=mat ARG2=matTThis action is not part of PLUMED and was included by using a LOAD command More details
# Select landmarks fps:LANDMARK_SELECT_FPS... 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=distmatSelect a set of landmarks using farthest point sampling. More detailsNLANDMARKS=50 ...the number of landmarks that you would like to select
# Do a voronoi analysis to work out the closet point to each landmark voro:VORONOIARG=fps.distmat_rectThis action is not part of PLUMED and was included by using a LOAD command More details
# Take the exponential of the log weights weights:CUSTOMCalculate a combination of variables using a custom expression. More detailsARG1=a.logweightsthe input to this functionFUNC=exp(xthe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# Now calculate the weight of each point by multiplying the voronoi matrix by the vector of weights lwe:DOTARG1=voro ARG2=weightsThis action is not part of PLUMED and was included by using a LOAD command More details
# Run Sketch map smap:SKETCHMAP... 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 ...This action is not part of PLUMED and was included by using a LOAD command More detailsPrint quantities to a file. More detailsARG=smap_osample.coord-1,smap_osample.coord-2the input for this action is the scalar output from one or more other actionsFILE=smap_data.datthe name of the file on which to output these quantities