Project ID: plumID:22.016
Source: SurfaceFreeEnergy/FindOptimalParameters/FindOptimalOrderParameter/IceIh/plumed.dat
Originally used with PLUMED version: 2.8
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
...
=1-864:3
=0.065
=CUSTOM
=refcv
=env1h.pdb
=env2h.pdb
=env3h.pdb
=env4h.pdb
={CUBIC D_0=0.447 D_MAX=0.949}
... ENVIRONMENTSIMILARITY
The ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities: Quantity | Description |
refcv.morethan | the number of colvars that have a value more than a threshold |
refcv.mean | the mean of the colvars |
...
=1-864:3
=0.065
=CUSTOM
=refcv
=env1h.pdb
=env2h.pdb
=env3h.pdb
=env4h.pdb
={CUBIC D_0=0.447 D_MAX=0.949}
=3 =0.0001 =100
... ENVIRONMENTSIMILARITY
# ENVIRONMENTSIMILARITY ...
refcv_cmat: =1-864:3 =0.6535
The DISTANCE_MATRIX action with label refcv_cmat calculates the following quantities: Quantity | Description |
refcv_cmat.w | a matrix containing the weights for the bonds between each pair of atoms |
refcv_cmat.x | the projection of the bond on the x axis |
refcv_cmat.y | the projection of the bond on the y axis |
refcv_cmat.z | the projection of the bond on the z axis |
refcv_cmat.value | a matrix containing the weights for the bonds between each pair of atoms |
refcv_grp: =1-864:3
The GROUP action with label refcv_grp calculates somethingrefcv_ones: =288
The ONES action with label refcv_ones calculates the following quantities: Quantity | Description |
refcv_ones.value | a vector of ones with the required number of elements |
refcv_matenv1: =refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.6535-w)/17)*(exp(-((x--0.4486)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.1296)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.4585)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.004225
The CUSTOM action with label refcv_matenv1 calculates the following quantities: Quantity | Description |
refcv_matenv1.value | an arbitrary function |
refcv_env1: =refcv_matenv1,refcv_ones
The MATRIX_VECTOR_PRODUCT action with label refcv_env1 calculates the following quantities: Quantity | Description |
refcv_env1.value | the vector that is obtained by taking the product between the matrix and the vector that were input |
refcv_env1..#!custom | the names of the output components for this action depend on the actions input file see the example inputs below for details |
refcv_matenv2: =refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.6535-w)/17)*(exp(-((x--0.4486)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y--0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.1297)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x--0.2239)^2+(y-0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.4585)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.004225
The CUSTOM action with label refcv_matenv2 calculates the following quantities: Quantity | Description |
refcv_matenv2.value | an arbitrary function |
refcv_env2: =refcv_matenv2,refcv_ones
The MATRIX_VECTOR_PRODUCT action with label refcv_env2 calculates the following quantities: Quantity | Description |
refcv_env2.value | the vector that is obtained by taking the product between the matrix and the vector that were input |
refcv_env2..#!custom | the names of the output components for this action depend on the actions input file see the example inputs below for details |
refcv_matenv3: =refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.6535-w)/17)*(exp(-((x--0.4485)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.4585)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.004225
The CUSTOM action with label refcv_matenv3 calculates the following quantities: Quantity | Description |
refcv_matenv3.value | an arbitrary function |
refcv_env3: =refcv_matenv3,refcv_ones
The MATRIX_VECTOR_PRODUCT action with label refcv_env3 calculates the following quantities: Quantity | Description |
refcv_env3.value | the vector that is obtained by taking the product between the matrix and the vector that were input |
refcv_env3..#!custom | the names of the output components for this action depend on the actions input file see the example inputs below for details |
refcv_matenv4: =refcv_cmat.x,refcv_cmat.y,refcv_cmat.z,refcv_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.6535-w)/17)*(exp(-((x--0.4485)^2+(y-0)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x--0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0)^2+(z-0.4585)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.3891)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z--0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.3668)^2)/(4*0.004225))+exp(-((x-0.2246)^2+(y-0.389)^2+(z-0)^2)/(4*0.004225))+exp(-((x-0.4492)^2+(y-0)^2+(z-0)^2)/(4*0.004225
The CUSTOM action with label refcv_matenv4 calculates the following quantities: Quantity | Description |
refcv_matenv4.value | an arbitrary function |
refcv_env4: =refcv_matenv4,refcv_ones
The MATRIX_VECTOR_PRODUCT action with label refcv_env4 calculates the following quantities: Quantity | Description |
refcv_env4.value | the vector that is obtained by taking the product between the matrix and the vector that were input |
refcv_env4..#!custom | the names of the output components for this action depend on the actions input file see the example inputs below for details |
refcv: =refcv_env1,refcv_env2,refcv_env3,refcv_env4 =NO =v1,v2,v3,v4 =(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4
refcv_mt: =refcv ={CUBIC D_0=0.447 D_MAX=0.949}
The MORE_THAN action with label refcv_mt calculates the following quantities: Quantity | Description |
refcv_mt.value | a function that is one if the if the input is more than a threshold |
refcv_morethan: =refcv_mt =NO
The SUM action with label refcv_morethan calculates the following quantities: Quantity | Description |
refcv_morethan.value | the sum |
refcv_mean: =refcv =NO
# --- End of included input ---
The MEAN action with label refcv_mean calculates the following quantities: Quantity | Description |
refcv_mean.value | the sum |
hh: ...
=refcv
=-0.5
=2
=1000
=0.01
...
The HISTOGRAM action with label hh calculates the following quantities: Quantity | Description |
hh.value | the estimate of the histogram as a function of the argument that was obtained |
hh: ...
=refcv
=-0.5
=2
=1000
=0.01
=ndata =1 =0
...
# hh: HISTOGRAM ...
hh_weight: =1
The ONES action with label hh_weight calculates the following quantities: Quantity | Description |
hh_weight.value | a vector of ones with the required number of elements |
hh_kde_u: =refcv =-0.5 =2 =1000 =0.01
The KDE action with label hh_kde_u calculates the following quantities: Quantity | Description |
hh_kde_u.value | a function on a grid that was obtained by doing a Kernel Density Estimation using the input arguments |
hh_kde: =hh_kde_u =NO =x/288
The CUSTOM action with label hh_kde calculates the following quantities: Quantity | Description |
hh_kde.value | an arbitrary function |
hh_kdep: =hh_kde,hh_weight =x*y =NO
The CUSTOM action with label hh_kdep calculates the following quantities: Quantity | Description |
hh_kdep.value | an arbitrary function |
hh_u: =hh_kdep =1 =0
The ACCUMULATE action with label hh_u calculates the following quantities: Quantity | Description |
hh_u.value | a sum calculated from the time series of the input quantity |
hh_nsum: =hh_weight =1 =0
The ACCUMULATE action with label hh_nsum calculates the following quantities: Quantity | Description |
hh_nsum.value | a sum calculated from the time series of the input quantity |
hh: =hh_u,hh_nsum =x/y =NO
# --- End of included input ---
=hh =histo =100
The DUMPGRID action with label calculates something =1 =COLVAR