PLUMED-NEST-TEST-SITE

Project ID: plumID:24.023
Source: input_holo/7/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 somethingd1: 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
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: 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
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: 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
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: 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
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5: 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
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6: 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
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd7: 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
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomsd8: 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
The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomsd9: 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
The DISTANCE action with label d9 calculates the following quantities:
 Quantity   
 Description  
d9.value
the DISTANCE between this pair of atomsd10: 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

The DISTANCE action with label d10 calculates the following quantities:
 Quantity   
 Description  
d10.value
the DISTANCE between this pair of atomsd1n: 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
The CUSTOM action with label d1n calculates the following quantities:
 Quantity   
 Description  
d1n.value
an arbitrary functiond2n: 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
The CUSTOM action with label d2n calculates the following quantities:
 Quantity   
 Description  
d2n.value
an arbitrary functiond3n: 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
The CUSTOM action with label d3n calculates the following quantities:
 Quantity   
 Description  
d3n.value
an arbitrary functiond4n: 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
The CUSTOM action with label d4n calculates the following quantities:
 Quantity   
 Description  
d4n.value
an arbitrary functiond5n: 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
The CUSTOM action with label d5n calculates the following quantities:
 Quantity   
 Description  
d5n.value
an arbitrary functiond6n: 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
The CUSTOM action with label d6n calculates the following quantities:
 Quantity   
 Description  
d6n.value
an arbitrary functiond7n: 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
The CUSTOM action with label d7n calculates the following quantities:
 Quantity   
 Description  
d7n.value
an arbitrary functiond8n: 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
The CUSTOM action with label d8n calculates the following quantities:
 Quantity   
 Description  
d8n.value
an arbitrary functiond9n: 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
The CUSTOM action with label d9n calculates the following quantities:
 Quantity   
 Description  
d9n.value
an arbitrary functiond10n: 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
The CUSTOM action with label d10n calculates the following quantities:
 Quantity   
 Description  
d10n.value
an arbitrary functionhldaN: 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

The COMBINE action with label hldaN calculates the following quantities:
 Quantity   
 Description  
hldaN.value
a linear compbinationWO: 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
The GROUP action with label WO calculates somethingAWO: 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

The COORDINATION action with label AWO calculates the following quantities:
 Quantity   
 Description  
AWO.value
the value of the coordinationt1: 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
The TORSION action with label t1 calculates the following quantities:
 Quantity   
 Description  
t1.value
the TORSION involving these atomst2: 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
The TORSION action with label t2 calculates the following quantities:
 Quantity   
 Description  
t2.value
the TORSION involving these atomst3: 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
The TORSION action with label t3 calculates the following quantities:
 Quantity   
 Description  
t3.value
the TORSION involving these atomst4: 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
The TORSION action with label t4 calculates the following quantities:
 Quantity   
 Description  
t4.value
the TORSION involving these atomst5: 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
The TORSION action with label t5 calculates the following quantities:
 Quantity   
 Description  
t5.value
the TORSION involving these atomst6: 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
The TORSION action with label t6 calculates the following quantities:
 Quantity   
 Description  
t6.value
the TORSION involving these atomst7: 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
The TORSION action with label t7 calculates the following quantities:
 Quantity   
 Description  
t7.value
the TORSION involving these atomst8: 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
The TORSION action with label t8 calculates the following quantities:
 Quantity   
 Description  
t8.value
the TORSION involving these atomst9: 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
The TORSION action with label t9 calculates the following quantities:
 Quantity   
 Description  
t9.value
the TORSION involving these atomst10: 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

The TORSION action with label t10 calculates the following quantities:
 Quantity   
 Description  
t10.value
the TORSION involving these atomst-1: 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
The TORSION action with label t-1 calculates the following quantities:
 Quantity   
 Description  
t-1.value
the TORSION involving these atomst-2: 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

The TORSION action with label t-2 calculates the following quantities:
 Quantity   
 Description  
t-2.value
the TORSION involving these atomsene: ENERGYCalculate the total potential energy of the simulation box. More details

The ENERGY action with label ene calculates somethingecv: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. 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=320
The ECV_MULTITHERMAL action with label ecv calculates the following quantities:
 Quantity   
 Description  
ecv..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsopesX: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. 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


The OPES_EXPANDED action with label opesX calculates the following quantities:
 Quantity   
 Description  
opesX.bias
the instantaneous value of the bias potentialOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
opes.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opesE1 calculates the following quantities:
 Quantity   
 Description  
opesE1.bias
the instantaneous value of the bias potential
opesE1.rct
estimate of c(t)
opesE1.zed
estimate of Z_n
opesE1.neff
effective sample size
opesE1.nker
total number of compressed kernels used to represent the bias
opesE1.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opesE2 calculates the following quantities:
 Quantity   
 Description  
opesE2.bias
the instantaneous value of the bias potential
opesE2.rct
estimate of c(t)
opesE2.zed
estimate of Z_n
opesE2.neff
effective sample size
opesE2.nker
total number of compressed kernels used to represent the bias
opesE2.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opesE3 calculates the following quantities:
 Quantity   
 Description  
opesE3.bias
the instantaneous value of the bias potential
opesE3.rct
estimate of c(t)
opesE3.zed
estimate of Z_n
opesE3.neff
effective sample size
opesE3.nker
total number of compressed kernels used to represent the bias
opesE3.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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
... OPES_METAD_EXPLORE


The OPES_METAD_EXPLORE action with label opesE4 calculates the following quantities:
 Quantity   
 Description  
opesE4.bias
the instantaneous value of the bias potential
opesE4.rct
estimate of c(t)
opesE4.zed
estimate of Z_n
opesE4.neff
effective sample size
opesE4.nker
total number of compressed kernels used to represent the bias
opesE4.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opesE5 calculates the following quantities:
 Quantity   
 Description  
opesE5.bias
the instantaneous value of the bias potential
opesE5.rct
estimate of c(t)
opesE5.zed
estimate of Z_n
opesE5.neff
effective sample size
opesE5.nker
total number of compressed kernels used to represent the bias
opesE5.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opesE6 calculates the following quantities:
 Quantity   
 Description  
opesE6.bias
the instantaneous value of the bias potential
opesE6.rct
estimate of c(t)
opesE6.zed
estimate of Z_n
opesE6.neff
effective sample size
opesE6.nker
total number of compressed kernels used to represent the bias
opesE6.work
total accumulated work done by the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=opesE7
  ARGthe labels of the scalars on which the bias will act=t7
  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=Kernels7.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels7
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels7
  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


The OPES_METAD_EXPLORE action with label opesE7 calculates the following quantities:
 Quantity   
 Description  
opesE7.bias
the instantaneous value of the bias potential
opesE7.rct
estimate of c(t)
opesE7.zed
estimate of Z_n
opesE7.neff
effective sample size
opesE7.nker
total number of compressed kernels used to represent the bias
opesE7.work
total accumulated work done by the biasPRINTPrint 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,opesE7.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