PLUMED-NEST

Project ID: plumID:24.023
Source: input_holo/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

RESTARTActivate restart. More details
#coefficents calculated between state 3 and 2

The RESTART action with label  calculates somethingd1The 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=243,751 #A-G
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=243,784 #A-C
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=243,787 #A-C
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/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=243,794 #A-RIB
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/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=243,800 #A-O
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/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=246,751 #A-G
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/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=246,784 #A-C
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/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=246,787 #A-C
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/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=246,794 #A-RIB
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/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=246,800 #A-O

d1nThe CUSTOM action with label d1n calculates the following quantities:
 Quantity   
 Type   
 Description  
d1n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1 FUNCthe function you wish to evaluate=x/2.11 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d2nThe CUSTOM action with label d2n calculates the following quantities:
 Quantity   
 Type   
 Description  
d2n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d2 FUNCthe function you wish to evaluate=x/2.25 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d3nThe CUSTOM action with label d3n calculates the following quantities:
 Quantity   
 Type   
 Description  
d3n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d3 FUNCthe function you wish to evaluate=x/2.17 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d4nThe CUSTOM action with label d4n calculates the following quantities:
 Quantity   
 Type   
 Description  
d4n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d4 FUNCthe function you wish to evaluate=x/2.53 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d5nThe CUSTOM action with label d5n calculates the following quantities:
 Quantity   
 Type   
 Description  
d5n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d5 FUNCthe function you wish to evaluate=x/2.78 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d6nThe CUSTOM action with label d6n calculates the following quantities:
 Quantity   
 Type   
 Description  
d6n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d6 FUNCthe function you wish to evaluate=x/2.07 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d7nThe CUSTOM action with label d7n calculates the following quantities:
 Quantity   
 Type   
 Description  
d7n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d7 FUNCthe function you wish to evaluate=x/2.22 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d8nThe CUSTOM action with label d8n calculates the following quantities:
 Quantity   
 Type   
 Description  
d8n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d8 FUNCthe function you wish to evaluate=x/2.13 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d9nThe CUSTOM action with label d9n calculates the following quantities:
 Quantity   
 Type   
 Description  
d9n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d1 FUNCthe function you wish to evaluate=x/2.49 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
d10nThe CUSTOM action with label d10n calculates the following quantities:
 Quantity   
 Type   
 Description  
d10n
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=d10 FUNCthe function you wish to evaluate=x/2.71 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO


#hlda: COMBINE ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10 COEFFICIENTS=-14.815268,-15.319241,-13.384423,-7.26893,-7.971926,-16.557427,-14.808337,-14.668623,-9.334746,-9.811748 PERIODIC=NO
hldaNThe COMBINE action with label hldaN calculates the following quantities:
 Quantity   
 Type   
 Description  
hldaN
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1n,d2n,d3n,d4n,d5n,d6n,d7n,d8n,d9n,d10n COEFFICIENTS the coefficients of the arguments in your function=-11.63344,-11.311855,-12.316635,-10.216072,-10.565613,-10.745473,-9.307333,-11.834765,-11.317639,-12.201419 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

WOThe GROUP action with label WO calculates the following quantities:
 Quantity   
 Type   
 Description  
WO
atoms
indices of atoms specified in GROUP: 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=1264-35692:4 # water molecules
AWOThe COORDINATION action with label AWO calculates the following quantities:
 Quantity   
 Type   
 Description  
AWO
scalar
the value of the coordination: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=243 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20

t1The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=225,228,229,232 #A, P-O-C-C
t2The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Type   
 Description  
t2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=228,229,232,251 #A, O-C-C-C
t3The TORSION action with label t3 calculates the following quantities:
 Quantity   
 Type   
 Description  
t3
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=229,232,251,257 #A C-C-C_O
t4The TORSION action with label t4 calculates the following quantities:
 Quantity   
 Type   
 Description  
t4
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=232,251,257,258 #A C-C-O-P
t5The TORSION action with label t5 calculates the following quantities:
 Quantity   
 Type   
 Description  
t5
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=251,257,258,261 #A C-O-P-O
t6The TORSION action with label t6 calculates the following quantities:
 Quantity   
 Type   
 Description  
t6
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=257,258,261,262 #A-C  O-P-O-C
t7The TORSION action with label t7 calculates the following quantities:
 Quantity   
 Type   
 Description  
t7
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=258,261,262,265 #C P-O-C-C
t8The TORSION action with label t8 calculates the following quantities:
 Quantity   
 Type   
 Description  
t8
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=261,262,265,282 #C O-C-C-C
t9The TORSION action with label t9 calculates the following quantities:
 Quantity   
 Type   
 Description  
t9
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=262,265,282,288 #C C-C-C-O
t10The TORSION action with label t10 calculates the following quantities:
 Quantity   
 Type   
 Description  
t10
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=265,282,288,289 #C C-C-O-P

t-1The TORSION action with label t-1 calculates the following quantities:
 Quantity   
 Type   
 Description  
t-1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=218,224,225,228 #G-A C-O-P-O
t-2The TORSION action with label t-2 calculates the following quantities:
 Quantity   
 Type   
 Description  
t-2
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=198,218,224,225 #G-A C-C-O-P

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

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_MINthe minimum of the temperature range=295 TEMP_MAXthe maximum of the temperature range=314
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_MINthe minimum of the temperature range=295 TEMP_MAXthe maximum of the temperature range=314  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: 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=200 UPDATE_FROMOnly update this action from this time=2000
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=200 UPDATE_FROMOnly update this action from this time=2000  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


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=hldaN
  SIGMA the initial widths of the kernels, divided by the square root of gamma=1
  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=20000
  BARRIERthe free energy barrier to be overcome=20
  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=hldaN
  SIGMA the initial widths of the kernels, divided by the square root of gamma=1
  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=20000
  BARRIERthe free energy barrier to be overcome=20
  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

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=opesE1The OPES_METAD_EXPLORE action with label opesE1 calculates the following quantities:
 Quantity   
 Type   
 Description  
opesE1.bias
scalar
the instantaneous value of the bias potential
opesE1.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesE1.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesE1.neff
scalar
effective sample size
opesE1.nker
scalar
total number of compressed kernels used to represent the bias
opesE1.work
scalar
total accumulated work done by the bias
  ARGthe labels of the scalars on which the bias will act=AWO
  SIGMA the initial widths of the kernels, divided by the square root of gamma=1
  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=compressed.Kernels1
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels1
  PACEthe frequency for kernel deposition=40000
  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
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=opesE1
  ARGthe labels of the scalars on which the bias will act=AWO
  SIGMA the initial widths of the kernels, divided by the square root of gamma=1
  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=compressed.Kernels1
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels1
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
  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

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=opesE2The OPES_METAD_EXPLORE action with label opesE2 calculates the following quantities:
 Quantity   
 Type   
 Description  
opesE2.bias
scalar
the instantaneous value of the bias potential
opesE2.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesE2.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesE2.neff
scalar
effective sample size
opesE2.nker
scalar
total number of compressed kernels used to represent the bias
opesE2.work
scalar
total accumulated work done by the bias
  ARGthe labels of the scalars on which the bias will act=t2
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1
  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=compressed.Kernels2
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels2
  PACEthe frequency for kernel deposition=40000
  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
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=opesE2
  ARGthe labels of the scalars on which the bias will act=t2
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1
  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=compressed.Kernels2
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels2
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
  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

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=opesE3The OPES_METAD_EXPLORE action with label opesE3 calculates the following quantities:
 Quantity   
 Type   
 Description  
opesE3.bias
scalar
the instantaneous value of the bias potential
opesE3.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesE3.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesE3.neff
scalar
effective sample size
opesE3.nker
scalar
total number of compressed kernels used to represent the bias
opesE3.work
scalar
total accumulated work done by the bias
  ARGthe labels of the scalars on which the bias will act=t3
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1
  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=compressed.Kernels3
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels3
  PACEthe frequency for kernel deposition=40000
  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
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=opesE3
  ARGthe labels of the scalars on which the bias will act=t3
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1
  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=compressed.Kernels3
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels3
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
  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

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=opesE4The OPES_METAD_EXPLORE action with label opesE4 calculates the following quantities:
 Quantity   
 Type   
 Description  
opesE4.bias
scalar
the instantaneous value of the bias potential
opesE4.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesE4.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesE4.neff
scalar
effective sample size
opesE4.nker
scalar
total number of compressed kernels used to represent the bias
opesE4.work
scalar
total accumulated work done by the bias
  ARGthe labels of the scalars on which the bias will act=t4
  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=Kernels4.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels4
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels4
  PACEthe frequency for kernel deposition=40000
  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
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=opesE4
  ARGthe labels of the scalars on which the bias will act=t4
  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=Kernels4.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels4
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels4
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
  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


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=opesE5The OPES_METAD_EXPLORE action with label opesE5 calculates the following quantities:
 Quantity   
 Type   
 Description  
opesE5.bias
scalar
the instantaneous value of the bias potential
opesE5.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesE5.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesE5.neff
scalar
effective sample size
opesE5.nker
scalar
total number of compressed kernels used to represent the bias
opesE5.work
scalar
total accumulated work done by the bias
  ARGthe labels of the scalars on which the bias will act=t5
  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=Kernels5.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels5
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels5
  PACEthe frequency for kernel deposition=40000
  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
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=opesE5
  ARGthe labels of the scalars on which the bias will act=t5
  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=Kernels5.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels5
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels5
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
  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

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=opesE6The OPES_METAD_EXPLORE action with label opesE6 calculates the following quantities:
 Quantity   
 Type   
 Description  
opesE6.bias
scalar
the instantaneous value of the bias potential
opesE6.rct
scalar
estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting
opesE6.zed
scalar
estimate of Z_n. should become flat once no new CV-space region is explored
opesE6.neff
scalar
effective sample size
opesE6.nker
scalar
total number of compressed kernels used to represent the bias
opesE6.work
scalar
total accumulated work done by the bias
  ARGthe labels of the scalars on which the bias will act=t6
  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=Kernels6.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels6
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels6
  PACEthe frequency for kernel deposition=40000
  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
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=opesE6
  ARGthe labels of the scalars on which the bias will act=t6
  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=Kernels6.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels6
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels6
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
  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


PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=hldaN,AWO,t2,t3,t4,t5,t6,ene,opes.bias,opesE1.bias,opesE2.bias,opesE3.bias,opesE4.bias,opesE5.bias,opesE6.bias,opesX.bias FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500