PLUMED-NEST-TEST-SITE by plumed-nest

Project ID: plumID:25.003
Source: Alanine_dipeptide/OPES_Flooding/plumed_kinetics.dat
Originally used with PLUMED version: 2.10
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
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=input.ala2.pdb
The MOLINFO action with label  calculates somethingphiThe TORSION action with label phi calculates the following quantities: Quantity    Type    Description  
phi scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@phi-2the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
psiThe TORSION action with label psi calculates the following quantities: Quantity    Type    Description  
psi scalar the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@psi-2the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
eneThe ENERGY action with label ene calculates the following quantities: Quantity    Type    Description  
ene scalar the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details


#DEFINE INPUTS: DISTANCES
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,5
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,6
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,7
d4The DISTANCE action with label d4 calculates the following quantities: Quantity    Type    Description  
d4 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,9
d5The DISTANCE action with label d5 calculates the following quantities: Quantity    Type    Description  
d5 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,11
d6The DISTANCE action with label d6 calculates the following quantities: Quantity    Type    Description  
d6 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,15
d7The DISTANCE action with label d7 calculates the following quantities: Quantity    Type    Description  
d7 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,16
d8The DISTANCE action with label d8 calculates the following quantities: Quantity    Type    Description  
d8 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,17
d9The DISTANCE action with label d9 calculates the following quantities: Quantity    Type    Description  
d9 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,19
d10The DISTANCE action with label d10 calculates the following quantities: Quantity    Type    Description  
d10 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6
d11The DISTANCE action with label d11 calculates the following quantities: Quantity    Type    Description  
d11 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,7
d12The DISTANCE action with label d12 calculates the following quantities: Quantity    Type    Description  
d12 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9
d13The DISTANCE action with label d13 calculates the following quantities: Quantity    Type    Description  
d13 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,11
d14The DISTANCE action with label d14 calculates the following quantities: Quantity    Type    Description  
d14 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,15
d15The DISTANCE action with label d15 calculates the following quantities: Quantity    Type    Description  
d15 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,16
d16The DISTANCE action with label d16 calculates the following quantities: Quantity    Type    Description  
d16 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,17
d17The DISTANCE action with label d17 calculates the following quantities: Quantity    Type    Description  
d17 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,19
d18The DISTANCE action with label d18 calculates the following quantities: Quantity    Type    Description  
d18 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,7
d19The DISTANCE action with label d19 calculates the following quantities: Quantity    Type    Description  
d19 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,9
d20The DISTANCE action with label d20 calculates the following quantities: Quantity    Type    Description  
d20 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,11
d21The DISTANCE action with label d21 calculates the following quantities: Quantity    Type    Description  
d21 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,15
d22The DISTANCE action with label d22 calculates the following quantities: Quantity    Type    Description  
d22 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,16
d23The DISTANCE action with label d23 calculates the following quantities: Quantity    Type    Description  
d23 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,17
d24The DISTANCE action with label d24 calculates the following quantities: Quantity    Type    Description  
d24 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,19
d25The DISTANCE action with label d25 calculates the following quantities: Quantity    Type    Description  
d25 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,9
d26The DISTANCE action with label d26 calculates the following quantities: Quantity    Type    Description  
d26 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,11
d27The DISTANCE action with label d27 calculates the following quantities: Quantity    Type    Description  
d27 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,15
d28The DISTANCE action with label d28 calculates the following quantities: Quantity    Type    Description  
d28 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,16
d29The DISTANCE action with label d29 calculates the following quantities: Quantity    Type    Description  
d29 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,17
d30The DISTANCE action with label d30 calculates the following quantities: Quantity    Type    Description  
d30 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,19
d31The DISTANCE action with label d31 calculates the following quantities: Quantity    Type    Description  
d31 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,11
d32The DISTANCE action with label d32 calculates the following quantities: Quantity    Type    Description  
d32 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,15
d33The DISTANCE action with label d33 calculates the following quantities: Quantity    Type    Description  
d33 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,16
d34The DISTANCE action with label d34 calculates the following quantities: Quantity    Type    Description  
d34 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,17
d35The DISTANCE action with label d35 calculates the following quantities: Quantity    Type    Description  
d35 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,19
d36The DISTANCE action with label d36 calculates the following quantities: Quantity    Type    Description  
d36 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,15
d37The DISTANCE action with label d37 calculates the following quantities: Quantity    Type    Description  
d37 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,16
d38The DISTANCE action with label d38 calculates the following quantities: Quantity    Type    Description  
d38 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,17
d39The DISTANCE action with label d39 calculates the following quantities: Quantity    Type    Description  
d39 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,19
d40The DISTANCE action with label d40 calculates the following quantities: Quantity    Type    Description  
d40 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,16
d41The DISTANCE action with label d41 calculates the following quantities: Quantity    Type    Description  
d41 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,17
d42The DISTANCE action with label d42 calculates the following quantities: Quantity    Type    Description  
d42 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,19
d43The DISTANCE action with label d43 calculates the following quantities: Quantity    Type    Description  
d43 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,17
d44The DISTANCE action with label d44 calculates the following quantities: Quantity    Type    Description  
d44 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,19
d45The DISTANCE action with label d45 calculates the following quantities: Quantity    Type    Description  
d45 scalar the DISTANCE between this pair of atoms:  DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,19

#Deep-TDA CV
deepTDAThe PYTORCH_MODEL action with label deepTDA calculates the following quantities: Quantity    Type    Description  
deepTDA.node-0 scalar Model outputs  This is the 0th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=ala2_deepTDA.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45

#Surrogate Model of Deep-TDA CV 
lasso_TDAThe COMBINE action with label lasso_TDA calculates the following quantities: Quantity    Type    Description  
lasso_TDA scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d9,d19,d20,d21,d22,d23,d24,d25,d26,d28,d30,d33,d37,d38,d39, COEFFICIENTS the coefficients of the arguments in your function=4.2236,123.9035,-74.1519,-24.5484,-20.8633,-3.6156,-10.3116,-15.1608,36.7252,22.8718,8.6337,-1.8104,5.3758,-1.7865,-0.6806, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
 
lassoCV_TDAThe MATHEVAL action with label lassoCV_TDA calculates the following quantities: Quantity    Type    Description  
lassoCV_TDA scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=lasso_TDA FUNCthe function you wish to evaluate=x-6.1677 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#Deep-TICA CV
deepTICAThe PYTORCH_MODEL action with label deepTICA calculates the following quantities: Quantity    Type    Description  
deepTICA.node-0 scalar Model outputs  This is the 0th of these quantities
deepTICA.node-1 scalar Model outputs  This is the 1th of these quantities: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=ala2_deepTICA.ptc ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20,d21,d22,d23,d24,d25,d26,d27,d28,d29,d30,d31,d32,d33,d34,d35,d36,d37,d38,d39,d40,d41,d42,d43,d44,d45

#Surrogate Model of Deep-TICA CV
lasso_TICAThe COMBINE action with label lasso_TICA calculates the following quantities: Quantity    Type    Description  
lasso_TICA scalar a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d3,d5,d9,d11,d13,d16,d17,d19,d20,d21,d22,d23,d26,d27,d28,d30,d33,d34,d37,d38,d43,d44, COEFFICIENTS the coefficients of the arguments in your function=-2.1943,0.5962,0.2754,-0.4293,-0.7594,-0.1269,-1.7356,13.3339,-8.7770,-0.1922,-2.5192,-2.5143,3.1540,1.5354,1.8088,2.4623,-1.7945,0.2039,1.0735,-0.0421,-1.9173,-0.0261, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

lassoCV_TICAThe MATHEVAL action with label lassoCV_TICA calculates the following quantities: Quantity    Type    Description  
lassoCV_TICA scalar an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=lasso_TICA FUNCthe function you wish to evaluate=x+0.1539 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

#Excluded regions
chi_excThe CUSTOM action with label chi_exc calculates the following quantities: Quantity    Type    Description  
chi_exc scalar an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=deepTDA.node-0 FUNCthe function you wish to evaluate=step(x+1.0) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
#chi_exc: CUSTOM ARG=lassoCV_TDA FUNC=step(x+1.0) PERIODIC=NO
#chi_exc: CUSTOM ARG=deepTICA.node-0 FUNC=step(x+0.3) PERIODIC=NO
#chi_exc: CUSTOM ARG=lassoCV_TICA FUNC=step(x+0.3) PERIODIC=NO

OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opesThe OPES_METAD action with label opes calculates the following quantities: Quantity    Type    Description  
opes.bias scalar the instantaneous value of the bias potential
opes.rct scalar estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opes.zed scalar estimate of Z_n. should become flat once no new CV-space region is explored
opes.neff scalar effective sample size
opes.nker scalar total number of compressed kernels used to represent the bias
  ARGthe labels of the scalars on which the bias will act=deepTDA.node-0
  #ARG=lassoCV_TDA
  #ARG=deepTICA.node-0
  #ARG=lassoCV_TICA
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=25
  TEMP temperature=300
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
...
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes
  ARGthe labels of the scalars on which the bias will act=deepTDA.node-0
  #ARG=lassoCV_TDA
  #ARG=deepTICA.node-0
  #ARG=lassoCV_TICA
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=25
  TEMP temperature=300
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
 SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
...

COMMITTORDoes a committor analysis. More details ...
 ARGthe labels of the values which is being used to define the committor surface=deepTDA.node-0
 STRIDE the frequency with which the CVs are analyzed=5000
 BASIN_LL1List of lower limits for basin #=4.5
 BASIN_UL1List of upper limits for basin #=10.0
... COMMITTOR

#COMMITTOR ...
# ARG=lassoCV_TDA
# STRIDE=5000
#BASIN_LL1=3.5 
# BASIN_UL1=10.0
#... COMMITTOR

#COMMITTOR ...
# ARG=deepTICA.node-0
# STRIDE=5000
# BASIN_LL1=0.3 
# BASIN_UL1=1.5 
#... COMMITTOR

#COMMITTOR ...
# ARG=lassoCV_TICA
# STRIDE=5000
# BASIN_LL1=0.3 
# BASIN_UL1=1.5 
#... COMMITTOR

PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR ARGthe labels of the values that you would like to print to the file=opes.bias

ENDPLUMEDTerminate plumed input. More details
Quantity	Type	Description
phi	scalar	the TORSION involving these atoms
PLUMED-NEST-TEST-SITE

The public repository of the PLUMED consortium
