PLUMED-NEST-TEST-SITE

Project ID: plumID:21.006
Source: ala2-well_tempered-phi/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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

#+++++++++++++++++++++++++++++++++++++++++++++++++++#
#                                                   #
#  This input generates a well-tempered simulation  #
#  that samples along the phi collective variable   #
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#+++++++++++++++++++++++++++++++++++++++++++++++++++#

phiThe 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=5,7,9,15
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=7,9,15,17
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

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.nlker
scalar
number of kernels in the neighbor list
opes.nlsteps
scalar
number of steps from last neighbor list update: 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
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=50
  SIGMA the initial widths of the kernels=0.15
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State.data
  NLIST use neighbor list for kernels summation, faster but experimental
...
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=phi
  FILE a file in which the list of all deposited kernels is stored=Kernels.data
  PACEthe frequency for kernel deposition=500
  BARRIERthe free energy barrier to be overcome=50
  SIGMA the initial widths of the kernels=0.15
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State.data
  NLIST use neighbor list for kernels summation, faster but experimental
 TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
...

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=500 FILEthe name of the file on which to output these quantities=Colvar.data ARGthe labels of the values that you would like to print to the file=phi,psi,ene,opes.bias,opes.rct,opes.zed,opes.nker

The PRINT action with label  calculates somethingENDPLUMEDTerminate plumed input. More details

If no SIGMA is provided, it will be automatically guessed.
The option NLIST activates a neighbor list that speeds up the computation.

The main advantage of using OPES_METAD over a multiumbrella OPES_EXPANDED is that it is much easier to handle multiple collective variables.