PLUMED-NEST

Project ID: plumID:21.023
Source: Data-ala1/ala1-vacuum-wtm-rct-ustride-1-bf5/plumed.dat
Originally used with PLUMED version: 2.7
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

energyThe ENERGY action with label energy calculates the following quantities:
 Quantity   
 Type   
 Description  
energy
scalar
the internal energy:   ENERGYCalculate the total potential energy of the simulation box. More details
phiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
the TORSION involving these atoms:      TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15    NOPBC ignore the periodic boundary conditions when calculating distances
psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms:      TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=7,9,15,17   NOPBC ignore the periodic boundary conditions when calculating distances
thetaThe TORSION action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
scalar
the TORSION involving these atoms:    TORSIONCalculate a torsional angle. More details ATOMSthe four atoms involved in the torsional angle=6,5,7,9     NOPBC ignore the periodic boundary conditions when calculating distances
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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,5        NOPBC ignore the periodic boundary conditions when calculating distances
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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,6        NOPBC ignore the periodic boundary conditions when calculating distances
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 between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,7        NOPBC ignore the periodic boundary conditions when calculating distances
d4The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Type   
 Description  
d4
scalar
the DISTANCE between this pair of atoms:       DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,9        NOPBC ignore the periodic boundary conditions when calculating distances
d5The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Type   
 Description  
d5
scalar
the DISTANCE between this pair of atoms:       DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,11       NOPBC ignore the periodic boundary conditions when calculating distances
d6The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Type   
 Description  
d6
scalar
the DISTANCE between this pair of atoms:       DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,15       NOPBC ignore the periodic boundary conditions when calculating distances
d7The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Type   
 Description  
d7
scalar
the DISTANCE between this pair of atoms:       DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,16       NOPBC ignore the periodic boundary conditions when calculating distances
d8The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Type   
 Description  
d8
scalar
the DISTANCE between this pair of atoms:       DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,17       NOPBC ignore the periodic boundary conditions when calculating distances
d9The DISTANCE action with label d9 calculates the following quantities:
 Quantity   
 Type   
 Description  
d9
scalar
the DISTANCE between this pair of atoms:       DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,19       NOPBC ignore the periodic boundary conditions when calculating distances
d10The DISTANCE action with label d10 calculates the following quantities:
 Quantity   
 Type   
 Description  
d10
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6        NOPBC ignore the periodic boundary conditions when calculating distances
d11The DISTANCE action with label d11 calculates the following quantities:
 Quantity   
 Type   
 Description  
d11
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,7        NOPBC ignore the periodic boundary conditions when calculating distances
d12The DISTANCE action with label d12 calculates the following quantities:
 Quantity   
 Type   
 Description  
d12
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,9        NOPBC ignore the periodic boundary conditions when calculating distances
d13The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Type   
 Description  
d13
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,11       NOPBC ignore the periodic boundary conditions when calculating distances
d14The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Type   
 Description  
d14
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,15       NOPBC ignore the periodic boundary conditions when calculating distances
d15The DISTANCE action with label d15 calculates the following quantities:
 Quantity   
 Type   
 Description  
d15
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,16       NOPBC ignore the periodic boundary conditions when calculating distances
d16The DISTANCE action with label d16 calculates the following quantities:
 Quantity   
 Type   
 Description  
d16
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,17       NOPBC ignore the periodic boundary conditions when calculating distances
d17The DISTANCE action with label d17 calculates the following quantities:
 Quantity   
 Type   
 Description  
d17
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,19       NOPBC ignore the periodic boundary conditions when calculating distances
d18The DISTANCE action with label d18 calculates the following quantities:
 Quantity   
 Type   
 Description  
d18
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,7        NOPBC ignore the periodic boundary conditions when calculating distances
d19The DISTANCE action with label d19 calculates the following quantities:
 Quantity   
 Type   
 Description  
d19
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,9        NOPBC ignore the periodic boundary conditions when calculating distances
d20The DISTANCE action with label d20 calculates the following quantities:
 Quantity   
 Type   
 Description  
d20
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,11       NOPBC ignore the periodic boundary conditions when calculating distances
d21The DISTANCE action with label d21 calculates the following quantities:
 Quantity   
 Type   
 Description  
d21
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,15       NOPBC ignore the periodic boundary conditions when calculating distances
d22The DISTANCE action with label d22 calculates the following quantities:
 Quantity   
 Type   
 Description  
d22
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,16       NOPBC ignore the periodic boundary conditions when calculating distances
d23The DISTANCE action with label d23 calculates the following quantities:
 Quantity   
 Type   
 Description  
d23
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,17       NOPBC ignore the periodic boundary conditions when calculating distances
d24The DISTANCE action with label d24 calculates the following quantities:
 Quantity   
 Type   
 Description  
d24
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=6,19       NOPBC ignore the periodic boundary conditions when calculating distances
d25The DISTANCE action with label d25 calculates the following quantities:
 Quantity   
 Type   
 Description  
d25
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,9        NOPBC ignore the periodic boundary conditions when calculating distances
d26The DISTANCE action with label d26 calculates the following quantities:
 Quantity   
 Type   
 Description  
d26
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,11       NOPBC ignore the periodic boundary conditions when calculating distances
d27The DISTANCE action with label d27 calculates the following quantities:
 Quantity   
 Type   
 Description  
d27
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,15       NOPBC ignore the periodic boundary conditions when calculating distances
d28The DISTANCE action with label d28 calculates the following quantities:
 Quantity   
 Type   
 Description  
d28
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,16       NOPBC ignore the periodic boundary conditions when calculating distances
d29The DISTANCE action with label d29 calculates the following quantities:
 Quantity   
 Type   
 Description  
d29
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,17       NOPBC ignore the periodic boundary conditions when calculating distances
d30The DISTANCE action with label d30 calculates the following quantities:
 Quantity   
 Type   
 Description  
d30
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=7,19       NOPBC ignore the periodic boundary conditions when calculating distances
d31The DISTANCE action with label d31 calculates the following quantities:
 Quantity   
 Type   
 Description  
d31
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,11       NOPBC ignore the periodic boundary conditions when calculating distances
d32The DISTANCE action with label d32 calculates the following quantities:
 Quantity   
 Type   
 Description  
d32
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,15       NOPBC ignore the periodic boundary conditions when calculating distances
d33The DISTANCE action with label d33 calculates the following quantities:
 Quantity   
 Type   
 Description  
d33
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,16       NOPBC ignore the periodic boundary conditions when calculating distances
d34The DISTANCE action with label d34 calculates the following quantities:
 Quantity   
 Type   
 Description  
d34
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,17       NOPBC ignore the periodic boundary conditions when calculating distances
d35The DISTANCE action with label d35 calculates the following quantities:
 Quantity   
 Type   
 Description  
d35
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=9,19       NOPBC ignore the periodic boundary conditions when calculating distances
d36The DISTANCE action with label d36 calculates the following quantities:
 Quantity   
 Type   
 Description  
d36
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,15      NOPBC ignore the periodic boundary conditions when calculating distances
d37The DISTANCE action with label d37 calculates the following quantities:
 Quantity   
 Type   
 Description  
d37
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,16      NOPBC ignore the periodic boundary conditions when calculating distances
d38The DISTANCE action with label d38 calculates the following quantities:
 Quantity   
 Type   
 Description  
d38
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,17      NOPBC ignore the periodic boundary conditions when calculating distances
d39The DISTANCE action with label d39 calculates the following quantities:
 Quantity   
 Type   
 Description  
d39
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=11,19      NOPBC ignore the periodic boundary conditions when calculating distances
d40The DISTANCE action with label d40 calculates the following quantities:
 Quantity   
 Type   
 Description  
d40
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,16      NOPBC ignore the periodic boundary conditions when calculating distances
d41The DISTANCE action with label d41 calculates the following quantities:
 Quantity   
 Type   
 Description  
d41
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,17      NOPBC ignore the periodic boundary conditions when calculating distances
d42The DISTANCE action with label d42 calculates the following quantities:
 Quantity   
 Type   
 Description  
d42
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=15,19      NOPBC ignore the periodic boundary conditions when calculating distances
d43The DISTANCE action with label d43 calculates the following quantities:
 Quantity   
 Type   
 Description  
d43
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,17      NOPBC ignore the periodic boundary conditions when calculating distances
d44The DISTANCE action with label d44 calculates the following quantities:
 Quantity   
 Type   
 Description  
d44
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=16,19      NOPBC ignore the periodic boundary conditions when calculating distances
d45The DISTANCE action with label d45 calculates the following quantities:
 Quantity   
 Type   
 Description  
d45
scalar
the DISTANCE between this pair of atoms:      DISTANCECalculate the distance between a pair of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=17,19      NOPBC ignore the periodic boundary conditions when calculating distances

METADUsed to performed metadynamics on one or more collective variables. 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=mtdThe METAD action with label mtd calculates the following quantities:
 Quantity   
 Type   
 Description  
mtd.bias
scalar
the instantaneous value of the bias potential
mtd.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.
mtd.rct
scalar
the reweighting factor c(t).

  ARGthe labels of the scalars on which the bias will act=phi,psi
  PACEthe frequency for hill addition=500
  SIGMAthe widths of the Gaussian hills=0.2,0.2
  HEIGHTthe heights of the Gaussian hills=1.2

  BIASFACTORuse well tempered metadynamics and use this bias factor=5
  GRID_MINthe lower bounds for the grid=-pi,-pi
  GRID_MAXthe upper bounds for the grid=pi,pi
  GRID_BINthe number of bins for the grid=500,500
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=1
... METAD
METADUsed to performed metadynamics on one or more collective variables. 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=mtd

  ARGthe labels of the scalars on which the bias will act=phi,psi
  PACEthe frequency for hill addition=500
  SIGMAthe widths of the Gaussian hills=0.2,0.2
  HEIGHTthe heights of the Gaussian hills=1.2

  BIASFACTORuse well tempered metadynamics and use this bias factor=5
  GRID_MINthe lower bounds for the grid=-pi,-pi
  GRID_MAXthe upper bounds for the grid=pi,pi
  GRID_BINthe number of bins for the grid=500,500
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=1
 FILE a file in which the list of added hills is stored=HILLS
... METAD

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