PLUMED-NEST

Project ID: plumID:25.008
Source: ala2/opes/plumed.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


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=../training/pytorch_models/ala2_with_koopman_lag0.1ps_trans1.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


 
METADUsed to performed metadynamics on one or more collective variables. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
  ARGthe labels of the scalars on which the bias will act=psi
  PACEthe frequency for hill addition=5000000
  HEIGHTthe heights of the Gaussian hills=1.2
  SIGMAthe widths of the Gaussian hills=0.05
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  FILE a file in which the list of added hills is stored=HILLS_trans1 #for forward transition CV
  #FILE=HILLS #for back-and-forth CV
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
...

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: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=deepTICA.node-0
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=20
...
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalars on which the bias will act=deepTICA.node-0
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=20
 TEMP temperature=-1 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
...

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=100 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=phi,psi,deepTICA.node-0,opes.*,metad.*

ENDPLUMEDTerminate plumed input. More details