Project ID: plumID:21.002
Source: Crystallization/IceIc/64molecules/350K/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
volThe VOLUME action with label vol calculates the following quantities: Quantity | Type | Description |
vol | scalar | the volume of simulation box |
:
...
=1-192:3
=0.050
=CUSTOM
=refcvThe ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities: Quantity | Type | Description |
refcv | vector | the environmental similar parameter for each of the input atoms |
refcv_morethan | scalar | the number of colvars that have a value more than a threshold |
refcv_mean | scalar | the mean of the colvars |
=env1c.pdb
=env2c.pdb
={RATIONAL R_0=0.5 NN=8 MM=16}
... ENVIRONMENTSIMILARITY
...
=1-192:3
=0.050
=CUSTOM
=refcv
=env1c.pdb
=env2c.pdb
={RATIONAL R_0=0.5 NN=8 MM=16}
=3 =0.0001 =100
... ENVIRONMENTSIMILARITY
# ENVIRONMENTSIMILARITY ...
refcv_cmatThe DISTANCE_MATRIX action with label refcv_cmat calculates the following quantities: Quantity | Type | Description |
refcv_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
refcv_cmat.x | matrix | the projection of the bond on the x axis |
refcv_cmat.y | matrix | the projection of the bond on the y axis |
refcv_cmat.z | matrix | the projection of the bond on the z axis |
: =1-192:3 =0.608629
refcv_grpThe GROUP action with label refcv_grp calculates the following quantities: Quantity | Type | Description |
refcv_grp | atoms | indices of atoms specified in GROUP |
: =1-192:3
refcv_onesThe CONSTANT action with label refcv_ones calculates the following quantities: Quantity | Type | Description |
refcv_ones | vector | the constant value that was read from the plumed input |
: =64
refcv_matenv1The CUSTOM action with label refcv_matenv1 calculates the following quantities: Quantity | Type | Description |
refcv_matenv1 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =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
refcv_env1The MATRIX_VECTOR_PRODUCT action with label refcv_env1 calculates the following quantities: Quantity | Type | Description |
refcv_env1 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv_matenv1,refcv_ones
refcv_matenv2The CUSTOM action with label refcv_matenv2 calculates the following quantities: Quantity | Type | Description |
refcv_matenv2 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =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
refcv_env2The MATRIX_VECTOR_PRODUCT action with label refcv_env2 calculates the following quantities: Quantity | Type | Description |
refcv_env2 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv_matenv2,refcv_ones
refcvThe CUSTOM action with label refcv calculates the following quantities: Quantity | Type | Description |
refcv | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: =refcv_env1,refcv_env2 =NO =v1,v2 =(1/100)*log(exp(100*v1)+exp(100*v2
refcv_mtThe MORE_THAN action with label refcv_mt calculates the following quantities: Quantity | Type | Description |
refcv_mt | vector | the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors |
: =refcv ={RATIONAL R_0=0.5 NN=8 MM=16}
refcv_morethanThe SUM action with label refcv_morethan calculates the following quantities: Quantity | Type | Description |
refcv_morethan | scalar | the sum of all the elements in the input vector |
: =refcv_mt =NO
refcv_meanThe MEAN action with label refcv_mean calculates the following quantities: Quantity | Type | Description |
refcv_mean | scalar | the mean of all the elements in the input vector |
: =refcv =NO
# --- End of included input ---
bf1: =40 =0.0 =64.0
The BF_LEGENDRE action with label bf1 calculates somethingtd_uni:
The TD_UNIFORM action with label td_uni calculates something ...
=refcv.morethan
=bf1
=350.0
=300
=td_uni
=b1The VES_LINEAR_EXPANSION action with label b1 calculates the following quantities: Quantity | Type | Description |
b1.bias | scalar | the instantaneous value of the bias potential |
b1.force2 | scalar | the instantaneous value of the squared force due to this bias potential. |
... VES_LINEAR_EXPANSION
...
=b1
=500
=o1
=1
=500
=500
=100
... OPT_AVERAGED_SGD
The OPT_AVERAGED_SGD action with label o1 calculates the following quantities: Quantity | Description |
o1.value | a scalar |
...
=b1
=500
=o1
=1
=500
=500
=100
=coeffs.data
... OPT_AVERAGED_SGD
=500 =COLVAR