Project ID: plumID:22.040
Source: mw-wtmeta-omi/plumed.dat
Originally used with PLUMED version: 2.8.0
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
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The WHOLEMOLECULES action with label calculates somethingpca1: =ref-v1.pdb =SIMPLE
# pca1: PCAVARS REFERENCE=ref-v1.pdb TYPE=SIMPLE
The PCAVARS action with label pca1 calculates the following quantities: Quantity | Description |
pca1.eig | the projections on the eigenvalues |
pca1.residual | the residual distance that is not projected on any of the eigenvalues |
pca1_at: =1 =ref-v1.pdb =SIMPLE
The RMSD action with label pca1_at calculates the following quantities: Quantity | Description |
pca1_at.value | the RMSD distance between the instaneous structure and the reference structure/s that were input |
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=1 =2400
The CONSTANT action with label pca1_peig calculates the following quantities: Quantity | Description |
pca1_peig.value | the constant value that was read from the plumed input |
pca1_eig: =pca1_peig,pca1_at.disp
The MATRIX_VECTOR_PRODUCT action with label pca1_eig calculates the following quantities: Quantity | Description |
pca1_eig.value | the vector that is obtained by taking the product between the matrix and the vector that were input |
pca1_eig..#!custom | the names of the output components for this action depend on the actions input file see the example inputs below for details |
pca1_eig-1: =pca1_eig =1
The SELECT_COMPONENTS action with label pca1_eig-1 calculates the following quantities: Quantity | Description |
pca1_eig-1.value | a vector containing the selected components |
pca1_eig2: =pca1_eig =x*x =NO
The CUSTOM action with label pca1_eig2 calculates the following quantities: Quantity | Description |
pca1_eig2.value | an arbitrary function |
pca1_eigsum2: =pca1_eig2 =NO
The SUM action with label pca1_eigsum2 calculates the following quantities: Quantity | Description |
pca1_eigsum2.value | the sum |
pca1_residual: =pca1_at.dist,pca1_eigsum2 =sqrt(x-y =NO
# --- End of included input --- The CUSTOM action with label pca1_residual calculates the following quantities: Quantity | Description |
pca1_residual.value | an arbitrary function |
pca2: =ref-v2.pdb =SIMPLE
# pca2: PCAVARS REFERENCE=ref-v2.pdb TYPE=SIMPLE
The PCAVARS action with label pca2 calculates the following quantities: Quantity | Description |
pca2.eig | the projections on the eigenvalues |
pca2.residual | the residual distance that is not projected on any of the eigenvalues |
pca2_at: =1 =ref-v2.pdb =SIMPLE
The RMSD action with label pca2_at calculates the following quantities: Quantity | Description |
pca2_at.value | the RMSD distance between the instaneous structure and the reference structure/s that were input |
pca2_peig: 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=1 =2400
The CONSTANT action with label pca2_peig calculates the following quantities: Quantity | Description |
pca2_peig.value | the constant value that was read from the plumed input |
pca2_eig: =pca2_peig,pca2_at.disp
The MATRIX_VECTOR_PRODUCT action with label pca2_eig calculates the following quantities: Quantity | Description |
pca2_eig.value | the vector that is obtained by taking the product between the matrix and the vector that were input |
pca2_eig..#!custom | the names of the output components for this action depend on the actions input file see the example inputs below for details |
pca2_eig-1: =pca2_eig =1
The SELECT_COMPONENTS action with label pca2_eig-1 calculates the following quantities: Quantity | Description |
pca2_eig-1.value | a vector containing the selected components |
pca2_eig2: =pca2_eig =x*x =NO
The CUSTOM action with label pca2_eig2 calculates the following quantities: Quantity | Description |
pca2_eig2.value | an arbitrary function |
pca2_eigsum2: =pca2_eig2 =NO
The SUM action with label pca2_eigsum2 calculates the following quantities: Quantity | Description |
pca2_eigsum2.value | the sum |
pca2_residual: =pca2_at.dist,pca2_eigsum2 =sqrt(x-y =NO
# --- End of included input ---
The CUSTOM action with label pca2_residual calculates the following quantities: Quantity | Description |
pca2_residual.value | an arbitrary function |
...
=meta
=pca1.eig-1,pca2.eig-1 =1.0,0.5 =0.2 =500
=15 =300
=-40,-15 =20,25 =150,150 =1000
... METAD
The METAD action with label meta calculates the following quantities: Quantity | Description |
meta.bias | the instantaneous value of the bias potential |
meta.rbias | the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct] |
meta.rct | the reweighting factor c(t) |
...
=meta
=pca1.eig-1,pca2.eig-1 =1.0,0.5 =0.2 =500
=15 =300
=-40,-15 =20,25 =150,150 =1000
=HILLS
... METAD
uw: =pca1.eig-1,pca2.eig-1 =15,20 =500,500
The UPPER_WALLS action with label uw calculates the following quantities: Quantity | Description |
uw.bias | the instantaneous value of the bias potential |
uw.force2 | the instantaneous value of the squared force due to this bias potential |
uw: =pca1.eig-1,pca2.eig-1 =15,20 =500,500 =0.0,0.0 =1.0,1.0 =2.0,2.0
# uw: UPPER_WALLS ARG=pca1.eig-1,pca2.eig-1 AT=15,20 KAPPA=500,500
uw_cv_pca1_eig-1: =NO =pca1.eig-1 =15
The COMBINE action with label uw_cv_pca1_eig-1 calculates the following quantities: Quantity | Description |
uw_cv_pca1_eig-1.value | a linear compbination |
uw_scale_pca1_eig-1: =NO =(x+0.0)/1.0 =uw_cv_pca1_eig-1
The CUSTOM action with label uw_scale_pca1_eig-1 calculates the following quantities: Quantity | Description |
uw_scale_pca1_eig-1.value | an arbitrary function |
uw_pow_pca1_eig-1: =NO =step(x)*x^2.0 =uw_scale_pca1_eig-1
The CUSTOM action with label uw_pow_pca1_eig-1 calculates the following quantities: Quantity | Description |
uw_pow_pca1_eig-1.value | an arbitrary function |
uw_v_wall_pca1_eig-1: =NO =500*x =uw_pow_pca1_eig-1
The CUSTOM action with label uw_v_wall_pca1_eig-1 calculates the following quantities: Quantity | Description |
uw_v_wall_pca1_eig-1.value | an arbitrary function |
uw_wall_pca1_eig-1: =uw_v_wall_pca1_eig-1 =NO
The SUM action with label uw_wall_pca1_eig-1 calculates the following quantities: Quantity | Description |
uw_wall_pca1_eig-1.value | the sum |
uw_force_pca1_eig-1: =NO =500*2.0*x/(y*1.0 =uw_pow_pca1_eig-1,uw_scale_pca1_eig-1
The CUSTOM action with label uw_force_pca1_eig-1 calculates the following quantities: Quantity | Description |
uw_force_pca1_eig-1.value | an arbitrary function |
uw_v_force2_pca1_eig-1: =NO =x*x =uw_force_pca1_eig-1
The CUSTOM action with label uw_v_force2_pca1_eig-1 calculates the following quantities: Quantity | Description |
uw_v_force2_pca1_eig-1.value | an arbitrary function |
uw_force2_pca1_eig-1: =uw_v_force2_pca1_eig-1 =NO
The SUM action with label uw_force2_pca1_eig-1 calculates the following quantities: Quantity | Description |
uw_force2_pca1_eig-1.value | the sum |
uw_cv_pca2_eig-1: =NO =pca2.eig-1 =20
The COMBINE action with label uw_cv_pca2_eig-1 calculates the following quantities: Quantity | Description |
uw_cv_pca2_eig-1.value | a linear compbination |
uw_scale_pca2_eig-1: =NO =(x+0.0)/1.0 =uw_cv_pca2_eig-1
The CUSTOM action with label uw_scale_pca2_eig-1 calculates the following quantities: Quantity | Description |
uw_scale_pca2_eig-1.value | an arbitrary function |
uw_pow_pca2_eig-1: =NO =step(x)*x^2.0 =uw_scale_pca2_eig-1
The CUSTOM action with label uw_pow_pca2_eig-1 calculates the following quantities: Quantity | Description |
uw_pow_pca2_eig-1.value | an arbitrary function |
uw_v_wall_pca2_eig-1: =NO =500*x =uw_pow_pca2_eig-1
The CUSTOM action with label uw_v_wall_pca2_eig-1 calculates the following quantities: Quantity | Description |
uw_v_wall_pca2_eig-1.value | an arbitrary function |
uw_wall_pca2_eig-1: =uw_v_wall_pca2_eig-1 =NO
The SUM action with label uw_wall_pca2_eig-1 calculates the following quantities: Quantity | Description |
uw_wall_pca2_eig-1.value | the sum |
uw_force_pca2_eig-1: =NO =500*2.0*x/(y*1.0 =uw_pow_pca2_eig-1,uw_scale_pca2_eig-1
The CUSTOM action with label uw_force_pca2_eig-1 calculates the following quantities: Quantity | Description |
uw_force_pca2_eig-1.value | an arbitrary function |
uw_v_force2_pca2_eig-1: =NO =x*x =uw_force_pca2_eig-1
The CUSTOM action with label uw_v_force2_pca2_eig-1 calculates the following quantities: Quantity | Description |
uw_v_force2_pca2_eig-1.value | an arbitrary function |
uw_force2_pca2_eig-1: =uw_v_force2_pca2_eig-1 =NO
The SUM action with label uw_force2_pca2_eig-1 calculates the following quantities: Quantity | Description |
uw_force2_pca2_eig-1.value | the sum |
uw_bias: =NO =uw_wall_pca1_eig-1,uw_wall_pca2_eig-1
The COMBINE action with label uw_bias calculates the following quantities: Quantity | Description |
uw_bias.value | a linear compbination |
=uw_bias
uw_force2: =NO =uw_force2_pca1_eig-1,uw_force2_pca2_eig-1
# --- End of included input --- The COMBINE action with label uw_force2 calculates the following quantities: Quantity | Description |
uw_force2.value | a linear compbination |
lw: =pca1.eig-1,pca2.eig-1 =-35,-12 =500,500
The LOWER_WALLS action with label lw calculates the following quantities: Quantity | Description |
lw.bias | the instantaneous value of the bias potential |
lw.force2 | the instantaneous value of the squared force due to this bias potential |
lw: =pca1.eig-1,pca2.eig-1 =-35,-12 =500,500 =0.0,0.0 =1.0,1.0 =2.0,2.0
# lw: LOWER_WALLS ARG=pca1.eig-1,pca2.eig-1 AT=-35,-12 KAPPA=500,500
lw_cv_pca1_eig-1: =NO =pca1.eig-1 =-35
The COMBINE action with label lw_cv_pca1_eig-1 calculates the following quantities: Quantity | Description |
lw_cv_pca1_eig-1.value | a linear compbination |
lw_scale_pca1_eig-1: =NO =(x-0.0)/1.0 =lw_cv_pca1_eig-1
The CUSTOM action with label lw_scale_pca1_eig-1 calculates the following quantities: Quantity | Description |
lw_scale_pca1_eig-1.value | an arbitrary function |
lw_pow_pca1_eig-1: =NO =step(-x)*x^2.0 =lw_scale_pca1_eig-1
The CUSTOM action with label lw_pow_pca1_eig-1 calculates the following quantities: Quantity | Description |
lw_pow_pca1_eig-1.value | an arbitrary function |
lw_v_wall_pca1_eig-1: =NO =500*x =lw_pow_pca1_eig-1
The CUSTOM action with label lw_v_wall_pca1_eig-1 calculates the following quantities: Quantity | Description |
lw_v_wall_pca1_eig-1.value | an arbitrary function |
lw_wall_pca1_eig-1: =lw_v_wall_pca1_eig-1 =NO
The SUM action with label lw_wall_pca1_eig-1 calculates the following quantities: Quantity | Description |
lw_wall_pca1_eig-1.value | the sum |
lw_force_pca1_eig-1: =NO =500*2.0*x/(y*1.0 =lw_pow_pca1_eig-1,lw_scale_pca1_eig-1
The CUSTOM action with label lw_force_pca1_eig-1 calculates the following quantities: Quantity | Description |
lw_force_pca1_eig-1.value | an arbitrary function |
lw_v_force2_pca1_eig-1: =NO =x*x =lw_force_pca1_eig-1
The CUSTOM action with label lw_v_force2_pca1_eig-1 calculates the following quantities: Quantity | Description |
lw_v_force2_pca1_eig-1.value | an arbitrary function |
lw_force2_pca1_eig-1: =lw_v_force2_pca1_eig-1 =NO
The SUM action with label lw_force2_pca1_eig-1 calculates the following quantities: Quantity | Description |
lw_force2_pca1_eig-1.value | the sum |
lw_cv_pca2_eig-1: =NO =pca2.eig-1 =-12
The COMBINE action with label lw_cv_pca2_eig-1 calculates the following quantities: Quantity | Description |
lw_cv_pca2_eig-1.value | a linear compbination |
lw_scale_pca2_eig-1: =NO =(x-0.0)/1.0 =lw_cv_pca2_eig-1
The CUSTOM action with label lw_scale_pca2_eig-1 calculates the following quantities: Quantity | Description |
lw_scale_pca2_eig-1.value | an arbitrary function |
lw_pow_pca2_eig-1: =NO =step(-x)*x^2.0 =lw_scale_pca2_eig-1
The CUSTOM action with label lw_pow_pca2_eig-1 calculates the following quantities: Quantity | Description |
lw_pow_pca2_eig-1.value | an arbitrary function |
lw_v_wall_pca2_eig-1: =NO =500*x =lw_pow_pca2_eig-1
The CUSTOM action with label lw_v_wall_pca2_eig-1 calculates the following quantities: Quantity | Description |
lw_v_wall_pca2_eig-1.value | an arbitrary function |
lw_wall_pca2_eig-1: =lw_v_wall_pca2_eig-1 =NO
The SUM action with label lw_wall_pca2_eig-1 calculates the following quantities: Quantity | Description |
lw_wall_pca2_eig-1.value | the sum |
lw_force_pca2_eig-1: =NO =500*2.0*x/(y*1.0 =lw_pow_pca2_eig-1,lw_scale_pca2_eig-1
The CUSTOM action with label lw_force_pca2_eig-1 calculates the following quantities: Quantity | Description |
lw_force_pca2_eig-1.value | an arbitrary function |
lw_v_force2_pca2_eig-1: =NO =x*x =lw_force_pca2_eig-1
The CUSTOM action with label lw_v_force2_pca2_eig-1 calculates the following quantities: Quantity | Description |
lw_v_force2_pca2_eig-1.value | an arbitrary function |
lw_force2_pca2_eig-1: =lw_v_force2_pca2_eig-1 =NO
The SUM action with label lw_force2_pca2_eig-1 calculates the following quantities: Quantity | Description |
lw_force2_pca2_eig-1.value | the sum |
lw_bias: =NO =lw_wall_pca1_eig-1,lw_wall_pca2_eig-1
The COMBINE action with label lw_bias calculates the following quantities: Quantity | Description |
lw_bias.value | a linear compbination |
=lw_bias
lw_force2: =NO =lw_force2_pca1_eig-1,lw_force2_pca2_eig-1
# --- End of included input ---
The COMBINE action with label lw_force2 calculates the following quantities: Quantity | Description |
lw_force2.value | a linear compbination |
=cv_all =500