Project ID: plumID:22.016
Source: SurfaceFreeEnergy/Basal/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
The RESTART action with label calculates something ...
=1-1728:3
=0.0675
=CUSTOM
=refcvThe ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities: Quantity | Type | Description |
refcv | vector | the value calculated by this action |
refcv_morethan | scalar | the number of colvars that have a value more than a threshold |
refcv_mean | scalar | the mean of the colvars |
=env1h.pdb
=env2h.pdb
=env3h.pdb
=env4h.pdb
={CUBIC D_0=0.60 D_MAX=0.98}
... ENVIRONMENTSIMILARITY
...
=1-1728:3
=0.0675
=CUSTOM
=refcv
=env1h.pdb
=env2h.pdb
=env3h.pdb
=env4h.pdb
={CUBIC D_0=0.60 D_MAX=0.98}
=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 |
: =1-1728:3 =0.477631
refcv_grpThe GROUP action with label refcv_grp calculates the following quantities: Quantity | Type | Description |
refcv_grp | atoms | indices of atoms specified in GROUP |
: =1-1728:3
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 |
: =576
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(0.477631-w)/4)*(exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.00455625
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(0.477631-w)/4)*(exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.00455625
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
refcv_matenv3The CUSTOM action with label refcv_matenv3 calculates the following quantities: Quantity | Type | Description |
refcv_matenv3 | 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(0.477631-w)/4)*(exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.00455625
refcv_env3The MATRIX_VECTOR_PRODUCT action with label refcv_env3 calculates the following quantities: Quantity | Type | Description |
refcv_env3 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv_matenv3,refcv_ones
refcv_matenv4The CUSTOM action with label refcv_matenv4 calculates the following quantities: Quantity | Type | Description |
refcv_matenv4 | 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(0.477631-w)/4)*(exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.00455625
refcv_env4The MATRIX_VECTOR_PRODUCT action with label refcv_env4 calculates the following quantities: Quantity | Type | Description |
refcv_env4 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv_matenv4,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,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_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 ={CUBIC D_0=0.60 D_MAX=0.98}
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 ---
sThe AROUND action with label s calculates the following quantities: Quantity | Type | Description |
s_mean | scalar | the average values of the colvar in the region of interest |
s_morethan | scalar | the number of cvs in the region of interest that are more than a certain threshold |
: =refcv =1 =-0.5 =0.5 =0.03 ={CUBIC D_0=0.60 D_MAX=0.98}
# s: AROUND DATA=refcv ATOM=1 ZLOWER=-0.5 ZUPPER=0.5 SIGMA=0.03 MEAN MORE_THAN={CUBIC D_0=0.60 D_MAX=0.98}
s_grpThe GROUP action with label s_grp calculates the following quantities: Quantity | Type | Description |
s_grp | atoms | indices of atoms specified in GROUP |
: =refcv
s_prodThe CUSTOM action with label s_prod calculates the following quantities: Quantity | Type | Description |
s_prod | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: =refcv,s =x*y =NO
s_numerThe SUM action with label s_numer calculates the following quantities: Quantity | Type | Description |
s_numer | scalar | the sum of all the elements in the input vector |
: =s_prod =NO
s_normThe SUM action with label s_norm calculates the following quantities: Quantity | Type | Description |
s_norm | scalar | the sum of all the elements in the input vector |
: =s =NO
s_meanThe CUSTOM action with label s_mean calculates the following quantities: Quantity | Type | Description |
s_mean | scalar | an arbitrary function |
: =s_numer,s_norm =x/y =NO
refcv_s_mtThe MORE_THAN action with label refcv_s_mt calculates the following quantities: Quantity | Type | Description |
refcv_s_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 ={CUBIC D_0=0.60 D_MAX=0.98}
s_mtThe CUSTOM action with label s_mt calculates the following quantities: Quantity | Type | Description |
s_mt | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: =refcv_s_mt,s =x*y =NO
s_morethanThe SUM action with label s_morethan calculates the following quantities: Quantity | Type | Description |
s_morethan | scalar | the sum of all the elements in the input vector |
: =s_mt =NO
# --- End of included input ---
...
=1
=4-1728:3
=0.0675
=CUSTOM
=refcv2The ENVIRONMENTSIMILARITY action with label refcv2 calculates the following quantities: Quantity | Type | Description |
refcv2 | vector | the value calculated by this action |
refcv2_morethan | scalar | the number of colvars that have a value more than a threshold |
refcv2_mean | scalar | the mean of the colvars |
=env1h.pdb
=env2h.pdb
=env3h.pdb
=env4h.pdb
={CUBIC D_0=0.60 D_MAX=0.98}
... ENVIRONMENTSIMILARITY
...
=1
=4-1728:3
=0.0675
=CUSTOM
=refcv2
=env1h.pdb
=env2h.pdb
=env3h.pdb
=env4h.pdb
={CUBIC D_0=0.60 D_MAX=0.98}
=3 =0.0001 =100
... ENVIRONMENTSIMILARITY
# ENVIRONMENTSIMILARITY ...
refcv2_cmatThe DISTANCE_MATRIX action with label refcv2_cmat calculates the following quantities: Quantity | Type | Description |
refcv2_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
refcv2_cmat.x | matrix | the projection of the bond on the x axis |
refcv2_cmat.y | matrix | the projection of the bond on the y axis |
refcv2_cmat.z | matrix | the projection of the bond on the z axis |
: =0.477631
refcv2_grpThe GROUP action with label refcv2_grp calculates the following quantities: Quantity | Type | Description |
refcv2_grp | atoms | indices of atoms specified in GROUP |
: =1
refcv2_onesThe CONSTANT action with label refcv2_ones calculates the following quantities: Quantity | Type | Description |
refcv2_ones | vector | the constant value that was read from the plumed input |
: =575
refcv2_matenv1The CUSTOM action with label refcv2_matenv1 calculates the following quantities: Quantity | Type | Description |
refcv2_matenv1 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.477631-w)/4)*(exp(-((x--0.2239)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0.2594)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y--0.1296)^2+(z--0.0917)^2)/(4*0.00455625
refcv2_env1The MATRIX_VECTOR_PRODUCT action with label refcv2_env1 calculates the following quantities: Quantity | Type | Description |
refcv2_env1 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv2_matenv1,refcv2_ones
refcv2_matenv2The CUSTOM action with label refcv2_matenv2 calculates the following quantities: Quantity | Type | Description |
refcv2_matenv2 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.477631-w)/4)*(exp(-((x--0.2239)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y--0.2594)^2+(z--0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z-0.2751)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y-0.1297)^2+(z--0.0917)^2)/(4*0.00455625
refcv2_env2The MATRIX_VECTOR_PRODUCT action with label refcv2_env2 calculates the following quantities: Quantity | Type | Description |
refcv2_env2 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv2_matenv2,refcv2_ones
refcv2_matenv3The CUSTOM action with label refcv2_matenv3 calculates the following quantities: Quantity | Type | Description |
refcv2_matenv3 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.477631-w)/4)*(exp(-((x--0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y--0.2594)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y-0.1296)^2+(z-0.0917)^2)/(4*0.00455625
refcv2_env3The MATRIX_VECTOR_PRODUCT action with label refcv2_env3 calculates the following quantities: Quantity | Type | Description |
refcv2_env3 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv2_matenv3,refcv2_ones
refcv2_matenv4The CUSTOM action with label refcv2_matenv4 calculates the following quantities: Quantity | Type | Description |
refcv2_matenv4 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv2_cmat.x,refcv2_cmat.y,refcv2_cmat.z,refcv2_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.477631-w)/4)*(exp(-((x--0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0)^2+(z--0.2751)^2)/(4*0.00455625))+exp(-((x-0)^2+(y-0.2594)^2+(z-0.0917)^2)/(4*0.00455625))+exp(-((x-0.2246)^2+(y--0.1297)^2+(z-0.0917)^2)/(4*0.00455625
refcv2_env4The MATRIX_VECTOR_PRODUCT action with label refcv2_env4 calculates the following quantities: Quantity | Type | Description |
refcv2_env4 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv2_matenv4,refcv2_ones
refcv2The CUSTOM action with label refcv2 calculates the following quantities: Quantity | Type | Description |
refcv2 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: =refcv2_env1,refcv2_env2,refcv2_env3,refcv2_env4 =NO =v1,v2,v3,v4 =(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4
refcv2_mtThe MORE_THAN action with label refcv2_mt calculates the following quantities: Quantity | Type | Description |
refcv2_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 |
: =refcv2 ={CUBIC D_0=0.60 D_MAX=0.98}
refcv2_morethanThe SUM action with label refcv2_morethan calculates the following quantities: Quantity | Type | Description |
refcv2_morethan | scalar | the sum of all the elements in the input vector |
: =refcv2_mt =NO
refcv2_meanThe MEAN action with label refcv2_mean calculates the following quantities: Quantity | Type | Description |
refcv2_mean | scalar | the mean of all the elements in the input vector |
: =refcv2 =NO
# --- End of included input ---
eneThe ENERGY action with label ene calculates the following quantities: Quantity | Type | Description |
ene | scalar | the value calculated by this action |
:
volThe VOLUME action with label vol calculates the following quantities: Quantity | Type | Description |
vol | scalar | the volume of simulation box |
:
=s.morethan,refcv2.morethan =500 =2 =312 =350
...
=1-1728:3
=0.08
=CUSTOM
=refcv3The ENVIRONMENTSIMILARITY action with label refcv3 calculates the following quantities: Quantity | Type | Description |
refcv3 | vector | the value calculated by this action |
refcv3_morethan | scalar | the number of colvars that have a value more than a threshold |
refcv3_mean | scalar | the mean of the colvars |
=env1c.pdb
=env2c.pdb
=env3c.pdb
=env4c.pdb
={CUBIC D_0=1.00 D_MAX=1.13}
... ENVIRONMENTSIMILARITY
...
=1-1728:3
=0.08
=CUSTOM
=refcv3
=env1c.pdb
=env2c.pdb
=env3c.pdb
=env4c.pdb
={CUBIC D_0=1.00 D_MAX=1.13}
=3 =0.0001 =100
... ENVIRONMENTSIMILARITY
# ENVIRONMENTSIMILARITY ...
refcv3_cmatThe DISTANCE_MATRIX action with label refcv3_cmat calculates the following quantities: Quantity | Type | Description |
refcv3_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
refcv3_cmat.x | matrix | the projection of the bond on the x axis |
refcv3_cmat.y | matrix | the projection of the bond on the y axis |
refcv3_cmat.z | matrix | the projection of the bond on the z axis |
: =1-1728:3 =0.698694
refcv3_grpThe GROUP action with label refcv3_grp calculates the following quantities: Quantity | Type | Description |
refcv3_grp | atoms | indices of atoms specified in GROUP |
: =1-1728:3
refcv3_onesThe CONSTANT action with label refcv3_ones calculates the following quantities: Quantity | Type | Description |
refcv3_ones | vector | the constant value that was read from the plumed input |
: =576
refcv3_matenv1The CUSTOM action with label refcv3_matenv1 calculates the following quantities: Quantity | Type | Description |
refcv3_matenv1 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv3_cmat.x,refcv3_cmat.y,refcv3_cmat.z,refcv3_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.698694-w)/16)*(exp(-((x--0.4585)^2+(y--0.0001)^2+(z-0.0019)^2)/(4*0.0064))+exp(-((x--0.2307)^2+(y--0.1316)^2+(z--0.3738)^2)/(4*0.0064))+exp(-((x--0.2296)^2+(y--0.1323)^2+(z--0.093)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y--0.3972)^2+(z-0)^2)/(4*0.0064))+exp(-((x--0.2292)^2+(y-0.397)^2+(z-0.0018)^2)/(4*0.0064))+exp(-((x--0.2278)^2+(y-0.1314)^2+(z-0.3756)^2)/(4*0.0064))+exp(-((x--0.0015)^2+(y-0.2655)^2+(z--0.3737)^2)/(4*0.0064))+exp(-((x--0.0003)^2+(y-0.2649)^2+(z--0.093)^2)/(4*0.0064))+exp(-((x-0.0012)^2+(y--0.0008)^2+(z-0.2809)^2)/(4*0.0064))+exp(-((x-0.0015)^2+(y--0.2657)^2+(z-0.3739)^2)/(4*0.0064))+exp(-((x-0.2278)^2+(y--0.1316)^2+(z--0.3756)^2)/(4*0.0064))+exp(-((x-0.229)^2+(y--0.1323)^2+(z--0.0948)^2)/(4*0.0064))+exp(-((x-0.2293)^2+(y-0.397)^2+(z-0)^2)/(4*0.0064))+exp(-((x-0.2294)^2+(y--0.3972)^2+(z--0.0018)^2)/(4*0.0064))+exp(-((x-0.2309)^2+(y-0.1314)^2+(z-0.3738)^2)/(4*0.0064))+exp(-((x-0.4586)^2+(y--0.0001)^2+(z--0.0018)^2)/(4*0.0064
refcv3_env1The MATRIX_VECTOR_PRODUCT action with label refcv3_env1 calculates the following quantities: Quantity | Type | Description |
refcv3_env1 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv3_matenv1,refcv3_ones
refcv3_matenv2The CUSTOM action with label refcv3_matenv2 calculates the following quantities: Quantity | Type | Description |
refcv3_matenv2 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv3_cmat.x,refcv3_cmat.y,refcv3_cmat.z,refcv3_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.698694-w)/16)*(exp(-((x--0.4586)^2+(y-0.0001)^2+(z-0.0018)^2)/(4*0.0064))+exp(-((x--0.2308)^2+(y--0.1315)^2+(z--0.3739)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y--0.3971)^2+(z--0.0001)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y-0.3971)^2+(z-0.0018)^2)/(4*0.0064))+exp(-((x--0.229)^2+(y-0.1322)^2+(z-0.0947)^2)/(4*0.0064))+exp(-((x--0.2278)^2+(y-0.1315)^2+(z-0.3756)^2)/(4*0.0064))+exp(-((x--0.0015)^2+(y-0.2657)^2+(z--0.3739)^2)/(4*0.0064))+exp(-((x--0.0012)^2+(y-0.0008)^2+(z--0.2809)^2)/(4*0.0064))+exp(-((x-0.0003)^2+(y--0.2649)^2+(z-0.093)^2)/(4*0.0064))+exp(-((x-0.0015)^2+(y--0.2655)^2+(z-0.3737)^2)/(4*0.0064))+exp(-((x-0.2278)^2+(y--0.1315)^2+(z--0.3757)^2)/(4*0.0064))+exp(-((x-0.2292)^2+(y--0.3971)^2+(z--0.0019)^2)/(4*0.0064))+exp(-((x-0.2293)^2+(y-0.3971)^2+(z--0.0001)^2)/(4*0.0064))+exp(-((x-0.2297)^2+(y-0.1322)^2+(z-0.0929)^2)/(4*0.0064))+exp(-((x-0.2307)^2+(y-0.1315)^2+(z-0.3737)^2)/(4*0.0064))+exp(-((x-0.4585)^2+(y-0.0001)^2+(z--0.0019)^2)/(4*0.0064
refcv3_env2The MATRIX_VECTOR_PRODUCT action with label refcv3_env2 calculates the following quantities: Quantity | Type | Description |
refcv3_env2 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv3_matenv2,refcv3_ones
refcv3_matenv3The CUSTOM action with label refcv3_matenv3 calculates the following quantities: Quantity | Type | Description |
refcv3_matenv3 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv3_cmat.x,refcv3_cmat.y,refcv3_cmat.z,refcv3_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.698694-w)/16)*(exp(-((x--0.4585)^2+(y--0.0001)^2+(z--0.0019)^2)/(4*0.0064))+exp(-((x--0.2307)^2+(y--0.1316)^2+(z-0.3738)^2)/(4*0.0064))+exp(-((x--0.2296)^2+(y--0.1323)^2+(z-0.093)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y--0.3972)^2+(z--0)^2)/(4*0.0064))+exp(-((x--0.2292)^2+(y-0.397)^2+(z--0.0018)^2)/(4*0.0064))+exp(-((x--0.2278)^2+(y-0.1314)^2+(z--0.3756)^2)/(4*0.0064))+exp(-((x--0.0015)^2+(y-0.2655)^2+(z-0.3737)^2)/(4*0.0064))+exp(-((x--0.0003)^2+(y-0.2649)^2+(z-0.093)^2)/(4*0.0064))+exp(-((x-0.0012)^2+(y--0.0008)^2+(z--0.2809)^2)/(4*0.0064))+exp(-((x-0.0015)^2+(y--0.2657)^2+(z--0.3739)^2)/(4*0.0064))+exp(-((x-0.2278)^2+(y--0.1316)^2+(z-0.3756)^2)/(4*0.0064))+exp(-((x-0.229)^2+(y--0.1323)^2+(z-0.0948)^2)/(4*0.0064))+exp(-((x-0.2293)^2+(y-0.397)^2+(z--0)^2)/(4*0.0064))+exp(-((x-0.2294)^2+(y--0.3972)^2+(z-0.0018)^2)/(4*0.0064))+exp(-((x-0.2309)^2+(y-0.1314)^2+(z--0.3738)^2)/(4*0.0064))+exp(-((x-0.4586)^2+(y--0.0001)^2+(z-0.0018)^2)/(4*0.0064
refcv3_env3The MATRIX_VECTOR_PRODUCT action with label refcv3_env3 calculates the following quantities: Quantity | Type | Description |
refcv3_env3 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv3_matenv3,refcv3_ones
refcv3_matenv4The CUSTOM action with label refcv3_matenv4 calculates the following quantities: Quantity | Type | Description |
refcv3_matenv4 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv3_cmat.x,refcv3_cmat.y,refcv3_cmat.z,refcv3_cmat.w =x,y,z,w =NO =(step(w-0.0001)*step(0.698694-w)/16)*(exp(-((x--0.4586)^2+(y-0.0001)^2+(z--0.0018)^2)/(4*0.0064))+exp(-((x--0.2308)^2+(y--0.1315)^2+(z-0.3739)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y--0.3971)^2+(z-0.0001)^2)/(4*0.0064))+exp(-((x--0.2293)^2+(y-0.3971)^2+(z--0.0018)^2)/(4*0.0064))+exp(-((x--0.229)^2+(y-0.1322)^2+(z--0.0947)^2)/(4*0.0064))+exp(-((x--0.2278)^2+(y-0.1315)^2+(z--0.3756)^2)/(4*0.0064))+exp(-((x--0.0015)^2+(y-0.2657)^2+(z-0.3739)^2)/(4*0.0064))+exp(-((x--0.0012)^2+(y-0.0008)^2+(z-0.2809)^2)/(4*0.0064))+exp(-((x-0.0003)^2+(y--0.2649)^2+(z--0.093)^2)/(4*0.0064))+exp(-((x-0.0015)^2+(y--0.2655)^2+(z--0.3737)^2)/(4*0.0064))+exp(-((x-0.2278)^2+(y--0.1315)^2+(z-0.3757)^2)/(4*0.0064))+exp(-((x-0.2292)^2+(y--0.3971)^2+(z-0.0019)^2)/(4*0.0064))+exp(-((x-0.2293)^2+(y-0.3971)^2+(z-0.0001)^2)/(4*0.0064))+exp(-((x-0.2297)^2+(y-0.1322)^2+(z--0.0929)^2)/(4*0.0064))+exp(-((x-0.2307)^2+(y-0.1315)^2+(z--0.3737)^2)/(4*0.0064))+exp(-((x-0.4585)^2+(y-0.0001)^2+(z-0.0019)^2)/(4*0.0064
refcv3_env4The MATRIX_VECTOR_PRODUCT action with label refcv3_env4 calculates the following quantities: Quantity | Type | Description |
refcv3_env4 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv3_matenv4,refcv3_ones
refcv3The CUSTOM action with label refcv3 calculates the following quantities: Quantity | Type | Description |
refcv3 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: =refcv3_env1,refcv3_env2,refcv3_env3,refcv3_env4 =NO =v1,v2,v3,v4 =(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4
refcv3_mtThe MORE_THAN action with label refcv3_mt calculates the following quantities: Quantity | Type | Description |
refcv3_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 |
: =refcv3 ={CUBIC D_0=1.00 D_MAX=1.13}
refcv3_morethanThe SUM action with label refcv3_morethan calculates the following quantities: Quantity | Type | Description |
refcv3_morethan | scalar | the sum of all the elements in the input vector |
: =refcv3_mt =NO
refcv3_meanThe MEAN action with label refcv3_mean calculates the following quantities: Quantity | Type | Description |
refcv3_mean | scalar | the mean of all the elements in the input vector |
: =refcv3 =NO
# --- End of included input ---
diffThe CUSTOM action with label diff calculates the following quantities: Quantity | Type | Description |
diff | scalar | an arbitrary function |
: =refcv.morethan,s.morethan =x-y =NO
uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities: Quantity | Type | Description |
uwall1.bias | scalar | the instantaneous value of the bias potential |
uwall1.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: =diff =50 =1.0 =2 =2
uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities: Quantity | Type | Description |
uwall2.bias | scalar | the instantaneous value of the bias potential |
uwall2.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: =refcv3.morethan =0 =20.0 =2 =4
diff2The CUSTOM action with label diff2 calculates the following quantities: Quantity | Type | Description |
diff2 | scalar | an arbitrary function |
: =s.morethan,refcv2.morethan =x/144-y/0.9 =NO
uwall3The UPPER_WALLS action with label uwall3 calculates the following quantities: Quantity | Type | Description |
uwall3.bias | scalar | the instantaneous value of the bias potential |
uwall3.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: =diff2 =0 =4000.0 =2 =2
...
=1-1728:3
=0.065
=CUSTOM
=refcv4The ENVIRONMENTSIMILARITY action with label refcv4 calculates the following quantities: Quantity | Type | Description |
refcv4 | vector | the value calculated by this action |
refcv4_morethan | scalar | the number of colvars that have a value more than a threshold |
refcv4_mean | scalar | the mean of the colvars |
=Large/env1h.pdb
=Large/env2h.pdb
=Large/env3h.pdb
=Large/env4h.pdb
={CUBIC D_0=0.65 D_MAX=0.67}
... ENVIRONMENTSIMILARITY
...
=1-1728:3
=0.065
=CUSTOM
=refcv4
=Large/env1h.pdb
=Large/env2h.pdb
=Large/env3h.pdb
=Large/env4h.pdb
={CUBIC D_0=0.65 D_MAX=0.67}
=3 =0.0001 =100
... ENVIRONMENTSIMILARITY
# ENVIRONMENTSIMILARITY ...
refcv4_cmatThe DISTANCE_MATRIX action with label refcv4_cmat calculates the following quantities: Quantity | Type | Description |
refcv4_cmat.w | matrix | a matrix containing the weights for the bonds between each pair of atoms |
refcv4_cmat.x | matrix | the projection of the bond on the x axis |
refcv4_cmat.y | matrix | the projection of the bond on the y axis |
refcv4_cmat.z | matrix | the projection of the bond on the z axis |
: =1-1728:3 =0.6535
refcv4_grpThe GROUP action with label refcv4_grp calculates the following quantities: Quantity | Type | Description |
refcv4_grp | atoms | indices of atoms specified in GROUP |
: =1-1728:3
refcv4_onesThe CONSTANT action with label refcv4_ones calculates the following quantities: Quantity | Type | Description |
refcv4_ones | vector | the constant value that was read from the plumed input |
: =576
refcv4_matenv1The CUSTOM action with label refcv4_matenv1 calculates the following quantities: Quantity | Type | Description |
refcv4_matenv1 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv4_cmat.x,refcv4_cmat.y,refcv4_cmat.z,refcv4_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
refcv4_env1The MATRIX_VECTOR_PRODUCT action with label refcv4_env1 calculates the following quantities: Quantity | Type | Description |
refcv4_env1 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv4_matenv1,refcv4_ones
refcv4_matenv2The CUSTOM action with label refcv4_matenv2 calculates the following quantities: Quantity | Type | Description |
refcv4_matenv2 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv4_cmat.x,refcv4_cmat.y,refcv4_cmat.z,refcv4_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
refcv4_env2The MATRIX_VECTOR_PRODUCT action with label refcv4_env2 calculates the following quantities: Quantity | Type | Description |
refcv4_env2 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv4_matenv2,refcv4_ones
refcv4_matenv3The CUSTOM action with label refcv4_matenv3 calculates the following quantities: Quantity | Type | Description |
refcv4_matenv3 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv4_cmat.x,refcv4_cmat.y,refcv4_cmat.z,refcv4_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
refcv4_env3The MATRIX_VECTOR_PRODUCT action with label refcv4_env3 calculates the following quantities: Quantity | Type | Description |
refcv4_env3 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv4_matenv3,refcv4_ones
refcv4_matenv4The CUSTOM action with label refcv4_matenv4 calculates the following quantities: Quantity | Type | Description |
refcv4_matenv4 | matrix | the matrix obtained by doing an element-wise application of an arbitrary function to the input matrix |
: =refcv4_cmat.x,refcv4_cmat.y,refcv4_cmat.z,refcv4_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
refcv4_env4The MATRIX_VECTOR_PRODUCT action with label refcv4_env4 calculates the following quantities: Quantity | Type | Description |
refcv4_env4 | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: =refcv4_matenv4,refcv4_ones
refcv4The CUSTOM action with label refcv4 calculates the following quantities: Quantity | Type | Description |
refcv4 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: =refcv4_env1,refcv4_env2,refcv4_env3,refcv4_env4 =NO =v1,v2,v3,v4 =(1/100)*log(exp(100*v1)+exp(100*v2)+exp(100*v3)+exp(100*v4
refcv4_mtThe MORE_THAN action with label refcv4_mt calculates the following quantities: Quantity | Type | Description |
refcv4_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 |
: =refcv4 ={CUBIC D_0=0.65 D_MAX=0.67}
refcv4_morethanThe SUM action with label refcv4_morethan calculates the following quantities: Quantity | Type | Description |
refcv4_morethan | scalar | the sum of all the elements in the input vector |
: =refcv4_mt =NO
refcv4_meanThe MEAN action with label refcv4_mean calculates the following quantities: Quantity | Type | Description |
refcv4_mean | scalar | the mean of all the elements in the input vector |
: =refcv4 =NO
# --- End of included input ---
s2The AROUND action with label s2 calculates the following quantities: Quantity | Type | Description |
s2_mean | scalar | the average values of the colvar in the region of interest |
s2_morethan | scalar | the number of cvs in the region of interest that are more than a certain threshold |
: =refcv4 =1 =-0.14 =0.14 =0.001 ={CUBIC D_0=0.65 D_MAX=0.67}
# s2: AROUND DATA=refcv4 ATOM=1 ZLOWER=-0.14 ZUPPER=0.14 SIGMA=0.001 MEAN MORE_THAN={CUBIC D_0=0.65 D_MAX=0.67}
s2_grpThe GROUP action with label s2_grp calculates the following quantities: Quantity | Type | Description |
s2_grp | atoms | indices of atoms specified in GROUP |
: =refcv4
s2_prodThe CUSTOM action with label s2_prod calculates the following quantities: Quantity | Type | Description |
s2_prod | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: =refcv4,s2 =x*y =NO
s2_numerThe SUM action with label s2_numer calculates the following quantities: Quantity | Type | Description |
s2_numer | scalar | the sum of all the elements in the input vector |
: =s2_prod =NO
s2_normThe SUM action with label s2_norm calculates the following quantities: Quantity | Type | Description |
s2_norm | scalar | the sum of all the elements in the input vector |
: =s2 =NO
s2_meanThe CUSTOM action with label s2_mean calculates the following quantities: Quantity | Type | Description |
s2_mean | scalar | an arbitrary function |
: =s2_numer,s2_norm =x/y =NO
refcv4_s2_mtThe MORE_THAN action with label refcv4_s2_mt calculates the following quantities: Quantity | Type | Description |
refcv4_s2_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 |
: =refcv4 ={CUBIC D_0=0.65 D_MAX=0.67}
s2_mtThe CUSTOM action with label s2_mt calculates the following quantities: Quantity | Type | Description |
s2_mt | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: =refcv4_s2_mt,s2 =x*y =NO
s2_morethanThe SUM action with label s2_morethan calculates the following quantities: Quantity | Type | Description |
s2_morethan | scalar | the sum of all the elements in the input vector |
: =s2_mt =NO
# --- End of included input ---
=500 =COLVAR