PLUMED-NEST

Project ID: plumID:22.031
Source: Ala2/phi/plumed.dat
Originally used with PLUMED version: 2.9
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

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=phi FUNCthe function you wish to evaluate=step(x+0.1) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

opesfThe OPES_METAD action with label opesf calculates the following quantities:
 Quantity   
 Type   
 Description  
opesf.bias
scalar
the instantaneous value of the bias potential
opesf.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesf.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesf.neff
scalar
effective sample size
opesf.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=phi
  PACEthe frequency for kernel deposition=500
  SIGMA the initial widths of the kernels=0.1 
  BARRIERthe free energy barrier to be overcome=20
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=500
...
opesf: 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=phi
  PACEthe frequency for kernel deposition=500
  SIGMA the initial widths of the kernels=0.1 
  BARRIERthe free energy barrier to be overcome=20
  EXCLUDED_REGIONkernels are not deposited when the action provided here has a nonzero value, see example above=chi_exc
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=500
 TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
...


COMMITTORDoes a committor analysis. More details ...
 ARGthe labels of the values which is being used to define the committor surface=phi
 STRIDE the frequency with which the CVs are analyzed=10
 BASIN_LL1List of lower limits for basin #=0.6
 BASIN_UL1List of upper limits for basin #=2.0
... 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=1 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,ene,opesf.*

ENDPLUMEDTerminate plumed input. More details