PLUMED-NEST

Project ID: plumID:24.020
Source: ala3/imetad/plumed_z1z2_1000.dat
Originally used with PLUMED version: 2.8.1
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

LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=Graph.cpp

The LOAD action with label  calculates somethingHEAVY: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1,5,6,7,9,11,15,16,17,19,21,25,26,27,29,31,35,36,37,39

The GROUP action with label HEAVY calculates somethingphi-1:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15       NOPBC ignore the periodic boundary conditions when calculating distances
# psi-1:   TORSION ATOMS=7,9,15,17      NOPBC
The TORSION action with label phi-1 calculates the following quantities:
 Quantity   
 Description  
phi-1.value
the TORSION involving these atomsphi-2:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,17,19,25    NOPBC ignore the periodic boundary conditions when calculating distances
# psi-2:   TORSION ATOMS=17,19,25,27    NOPBC
The TORSION action with label phi-2 calculates the following quantities:
 Quantity   
 Description  
phi-2.value
the TORSION involving these atomsphi-3:   TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=25,27,29,35    NOPBC ignore the periodic boundary conditions when calculating distances
# psi-3:   TORSION ATOMS=27,29,35,37    NOPBC

The TORSION action with label phi-3 calculates the following quantities:
 Quantity   
 Description  
phi-3.value
the TORSION involving these atomsGRAPHThis action is not part of PLUMED and was included by using a LOAD command More details ...
 LABEL=model
 ATOMS=HEAVY
 RCUT=5.0
 MODEL=model.pt
... GRAPH

METADUsed to performed metadynamics on one or more collective variables. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=mtd

  ARGthe labels of the scalars on which the bias will act=model.node-0,model.node-1
  PACEthe frequency for hill addition=1000
  SIGMAthe widths of the Gaussian hills=0.2,0.2
  HEIGHTthe heights of the Gaussian hills=1.65

  BIASFACTORuse well tempered metadynamics and use this bias factor=5
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=400
  GRID_MINthe lower bounds for the grid=-20,-20
  GRID_MAXthe upper bounds for the grid=20,15
  GRID_BINthe number of bins for the grid=500,500
  # CALC_RCT
  ACCELERATION Set to TRUE if you want to compute the metadynamics acceleration factor
  # RCT_USTRIDE=50
... METAD

The METAD action with label mtd calculates the following quantities:
 Quantity   
 Description  
mtd.bias
the instantaneous value of the bias potential
mtd.acc
the metadynamics acceleration factorCOMMITTORDoes a committor analysis. More details ...
  ARGthe labels of the values which is being used to define the committor surface=phi-1,phi-2,phi-3
  BASIN_UL1List of upper limits for basin #=-0.2pi,0.4pi,1.5
  BASIN_LL1List of lower limits for basin #=-0.6pi,0.2pi,0.5
  FILEthe name of the file on which to output the reached basin=PASS
... COMMITTOR

PRINTPrint quantities to a file. More details ...
  ARGthe labels of the values that you would like to print to the file=mtd.bias,mtd.acc
  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
... PRINT