Project ID: plumID:21.002
Source: CoexistenceSimulations/CoexistenceNNP/IceIc/Analyze/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
...
=1-1728:3
=0.05
=CUSTOM
=refcv
=env1c.pdb
=env2c.pdb
={RATIONAL R_0=0.5 NN=8 MM=16}
... 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 |
...
=1-1728:3
=0.05
=CUSTOM
=refcv
=env1c.pdb
=env2c.pdb
={RATIONAL R_0=0.5 NN=8 MM=16}
=3 =0.0001 =100
... ENVIRONMENTSIMILARITY
# ENVIRONMENTSIMILARITY ...
refcv_cmat: =1-1728:3 =0.608629
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: =1-1728:3
The GROUP action with label refcv_grp calculates somethingrefcv_ones: =576
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(0.608629-w)/16)*(exp(-((x--0.3243)^2+(y--0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.1622)^2+(y--0.1622)^2+(z-0.1621)^2)/(4*0.0025))+exp(-((x--0.1622)^2+(y-0.1621)^2+(z--0.1622)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3243)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3243)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3242)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3242)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y--0.1622)^2+(z--0.1622)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y-0.1621)^2+(z-0.1621)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y--0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z--0.3243)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z-0.3242)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0.3242)^2+(z-0)^2)/(4*0.0025
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(0.608629-w)/16)*(exp(-((x--0.3243)^2+(y--0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x--0.3243)^2+(y-0.3243)^2+(z-0)^2)/(4*0.0025))+exp(-((x--0.1621)^2+(y--0.1621)^2+(z--0.1621)^2)/(4*0.0025))+exp(-((x--0.1621)^2+(y-0.1622)^2+(z-0.1622)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3242)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y--0.3242)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3243)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0)^2+(y-0.3243)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y--0.1621)^2+(z-0.1622)^2)/(4*0.0025))+exp(-((x-0.1621)^2+(y-0.1622)^2+(z--0.1621)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y--0.3242)^2+(z-0)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z--0.3242)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0)^2+(z-0.3243)^2)/(4*0.0025))+exp(-((x-0.3242)^2+(y-0.3243)^2+(z-0)^2)/(4*0.0025
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: =refcv_env1,refcv_env2 =NO =v1,v2 =(1/100)*log(exp(100*v1)+exp(100*v2
refcv_mt: =refcv ={RATIONAL R_0=0.5 NN=8 MM=16}
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 |
energy:
The ENERGY action with label energy calculates somethingvol:
The VOLUME action with label vol calculates the volume of simulation box =500 =COLVAR