PLUMED-NEST

Project ID: plumID:23.011
Source: Alanine/OneOPES/5/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 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. 
omegaThe TORSION action with label omega calculates the following quantities:
 Quantity   
 Type   
 Description  
omega
scalar
the TORSION involving these atoms: 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. 
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

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=2,19
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=6,17
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=7,16

OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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_EXPLORE 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.work
scalar
total accumulated work done by the bias
  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_RFILE=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
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=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_RFILE=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
 TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD_EXPLORE

ecvThe ECV_MULTITHERMAL action with label ecv calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv.ene
scalar
the value of the argument named ene: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. This action has hidden defaults. More details ARGthe label of the internal energy of the system=ene TEMP_MAXthe maximum of the temperature range=600 
ecv: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. This action uses the defaults shown here. More details ARGthe label of the internal energy of the system=ene TEMP_MAXthe maximum of the temperature range=600  TEMP temperature=-1
opesXThe OPES_EXPANDED action with label opesX calculates the following quantities:
 Quantity   
 Type   
 Description  
opesX.bias
scalar
the instantaneous value of the bias potential
opesX.work
scalar
total accumulated work done by the bias: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. 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
opesX: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. 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  OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100

PRINTPrint 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,opes.work,opesX.work FMTthe format that should be used to output real numbers=%7.4f

ENDPLUMEDTerminate plumed input. More details