PLUMED-NEST

Project ID: plumID:23.011
Source: Alanine/OneOPES_MultiCV/6/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. 
#RESTART

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 somethingphi: 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. 
The TORSION action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomspsi: 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. 
The TORSION action with label psi calculates the following quantities:
 Quantity   
 Description  
psi.value
the TORSION involving these atomsomega: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=@omega-2the four atoms that are required to calculate the omega dihedral for residue 2. Click here for more information. 
The TORSION action with label omega calculates the following quantities:
 Quantity   
 Description  
omega.value
the TORSION involving these atomsene: ENERGYCalculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates somethingd1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,19
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,17
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,16

The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsecv: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. More details ARGthe label of the internal energy of the system=ene TEMP_MAXthe maximum of the temperature range=600
The ECV_MULTITHERMAL action with label ecv calculates the following quantities:
 Quantity   
 Description  
ecv..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsopesX: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details ARGthe label of the ECVs that define the expansion=ecv.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaFs.data PACEhow often the bias is updated=50 CALC_WORK calculate the total accumulated work done by the bias since last restart

The OPES_EXPANDED action with label opesX calculates the following quantities:
 Quantity   
 Description  
opesX.bias
the instantaneous value of the bias potential
opesX.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=psi
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2
  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
  PACEthe frequency for kernel deposition=5000
  BARRIERthe free energy barrier to be overcome=50
  CALC_WORK calculate the total accumulated work done by the bias since last restart
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
opes.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes1
  ARGthe labels of the scalars on which the bias will act=d1
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.02
  FILE a file in which the list of all deposited kernels is stored=Kernels1.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed1.Kernels
  PACEthe frequency for kernel deposition=10000
  BARRIERthe free energy barrier to be overcome=3
  CALC_WORK calculate the total accumulated work done by the bias since last restart
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes1 calculates the following quantities:
 Quantity   
 Description  
opes1.bias
the instantaneous value of the bias potential
opes1.rct
estimate of c(t)
opes1.zed
estimate of Z_n
opes1.neff
effective sample size
opes1.nker
total number of compressed kernels used to represent the bias
opes1.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes2
  ARGthe labels of the scalars on which the bias will act=d2
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.015
  FILE a file in which the list of all deposited kernels is stored=Kernels2.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed2.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed2.Kernels
  PACEthe frequency for kernel deposition=10000
  BARRIERthe free energy barrier to be overcome=3
  CALC_WORK calculate the total accumulated work done by the bias since last restart
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes2 calculates the following quantities:
 Quantity   
 Description  
opes2.bias
the instantaneous value of the bias potential
opes2.rct
estimate of c(t)
opes2.zed
estimate of Z_n
opes2.neff
effective sample size
opes2.nker
total number of compressed kernels used to represent the bias
opes2.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opes3
  ARGthe labels of the scalars on which the bias will act=d3
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.01
  FILE a file in which the list of all deposited kernels is stored=Kernels3.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed3.Kernels
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed3.Kernels
  PACEthe frequency for kernel deposition=10000
  BARRIERthe free energy barrier to be overcome=3
  CALC_WORK calculate the total accumulated work done by the bias since last restart
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes3 calculates the following quantities:
 Quantity   
 Description  
opes3.bias
the instantaneous value of the bias potential
opes3.rct
estimate of c(t)
opes3.zed
estimate of Z_n
opes3.neff
effective sample size
opes3.nker
total number of compressed kernels used to represent the bias
opes3.work
total accumulated work done by the biasPRINTPrint quantities to a file. More details 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=opes.bias,phi,psi,ene,omega,d1,d2,d3,opesX.bias,opes1.bias,opes2.bias,opes3.bias,opes.work,opesX.work,opes1.work,opes2.work,opes3.work FMTthe format that should be used to output real numbers=%7.4f

ENDPLUMEDTerminate plumed input. More details