PLUMED-NEST

Project ID: plumID:24.022
Source: ala2/infr_metad/template/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. 

cosphiThe MATHEVAL action with label cosphi calculates the following quantities:
 Quantity   
 Type   
 Description  
cosphi
scalar
an arbitrary function: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=phi FUNCthe function you wish to evaluate=0.5+cos(x-1.25) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

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=cosphi FUNCthe function you wish to evaluate=step(x-0.4) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
  ARGthe labels of the scalars on which the bias will act=cosphi
  PACEthe frequency for hill addition=5000
  HEIGHTthe heights of the Gaussian hills=1.2
  SIGMAthe widths of the Gaussian hills=0.02
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  GRID_MINthe lower bounds for the grid=-0.5 
  GRID_MAXthe upper bounds for the grid=1.5
  GRID_BINthe number of bins for the grid=200
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...
metad: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalars on which the bias will act=cosphi
  PACEthe frequency for hill addition=5000
  HEIGHTthe heights of the Gaussian hills=1.2
  SIGMAthe widths of the Gaussian hills=0.02
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  GRID_MINthe lower bounds for the grid=-0.5 
  GRID_MAXthe upper bounds for the grid=1.5
  GRID_BINthe number of bins for the grid=200
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 FILE a file in which the list of added hills is stored=HILLS
...


COMMITTORDoes a committor analysis. More details ...
 ARGthe labels of the values which is being used to define the committor surface=cosphi
 STRIDE the frequency with which the CVs are analyzed=1
 BASIN_LL1List of lower limits for basin #=1.4
 BASIN_UL1List of upper limits for basin #=1.6
... 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,cosphi,metad.*

ENDPLUMEDTerminate plumed input. More details