PLUMED-NEST-TEST-SITE

Project ID: plumID:24.019
Source: ala2/7-adaptive-40ps/opes/1/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

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.pdb
The MOLINFO action with label  calculates somethingpair1The DISTANCE action with label pair1 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair1
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=1,5
pair2The DISTANCE action with label pair2 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair2
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=1,6
pair3The DISTANCE action with label pair3 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair3
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=1,7
pair4The DISTANCE action with label pair4 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair4
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=1,9
pair5The DISTANCE action with label pair5 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair5
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=1,11
pair6The DISTANCE action with label pair6 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair6
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=1,15
pair7The DISTANCE action with label pair7 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair7
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=1,16
pair8The DISTANCE action with label pair8 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair8
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=1,17
pair9The DISTANCE action with label pair9 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair9
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=1,19
pair10The DISTANCE action with label pair10 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair10
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=5,6
pair11The DISTANCE action with label pair11 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair11
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=5,7
pair12The DISTANCE action with label pair12 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair12
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=5,9
pair13The DISTANCE action with label pair13 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair13
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=5,11
pair14The DISTANCE action with label pair14 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair14
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=5,15
pair15The DISTANCE action with label pair15 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair15
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=5,16
pair16The DISTANCE action with label pair16 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair16
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=5,17
pair17The DISTANCE action with label pair17 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair17
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=5,19
pair18The DISTANCE action with label pair18 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair18
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=6,7
pair19The DISTANCE action with label pair19 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair19
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=6,9
pair20The DISTANCE action with label pair20 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair20
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=6,11
pair21The DISTANCE action with label pair21 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair21
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=6,15
pair22The DISTANCE action with label pair22 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair22
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=6,16
pair23The DISTANCE action with label pair23 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair23
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=6,17
pair24The DISTANCE action with label pair24 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair24
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=6,19
pair25The DISTANCE action with label pair25 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair25
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=7,9
pair26The DISTANCE action with label pair26 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair26
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=7,11
pair27The DISTANCE action with label pair27 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair27
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=7,15
pair28The DISTANCE action with label pair28 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair28
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=7,16
pair29The DISTANCE action with label pair29 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair29
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=7,17
pair30The DISTANCE action with label pair30 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair30
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=7,19
pair31The DISTANCE action with label pair31 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair31
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=9,11
pair32The DISTANCE action with label pair32 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair32
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=9,15
pair33The DISTANCE action with label pair33 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair33
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=9,16
pair34The DISTANCE action with label pair34 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair34
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=9,17
pair35The DISTANCE action with label pair35 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair35
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=9,19
pair36The DISTANCE action with label pair36 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair36
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=11,15
pair37The DISTANCE action with label pair37 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair37
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=11,16
pair38The DISTANCE action with label pair38 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair38
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=11,17
pair39The DISTANCE action with label pair39 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair39
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=11,19
pair40The DISTANCE action with label pair40 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair40
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=15,16
pair41The DISTANCE action with label pair41 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair41
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=15,17
pair42The DISTANCE action with label pair42 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair42
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=15,19
pair43The DISTANCE action with label pair43 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair43
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=16,17
pair44The DISTANCE action with label pair44 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair44
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=16,19
pair45The DISTANCE action with label pair45 calculates the following quantities:
 Quantity   
 Type   
 Description  
pair45
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=17,19
tica0The COMBINE action with label tica0 calculates the following quantities:
 Quantity   
 Type   
 Description  
tica0
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=pair1,pair2,pair3,pair4,pair5,pair6,pair7,pair8,pair9,pair10,pair11,pair12,pair13,pair14,pair15,pair16,pair17,pair18,pair19,pair20,pair21,pair22,pair23,pair24,pair25,pair26,pair27,pair28,pair29,pair30,pair31,pair32,pair33,pair34,pair35,pair36,pair37,pair38,pair39,pair40,pair41,pair42,pair43,pair44,pair45 COEFFICIENTS the coefficients of the arguments in your function=-3.8789763558510995,2.5799568987291486,-5.107531852573498,1.2415414990120939,-0.23708900116095505,-7.845534788834517,3.4656825620718976,9.347634343839726,-1.3532086683415752,3.763318523199043,-2.0823713939080086,11.530520802126961,-2.0678238244656515,-0.7579221463696283,5.411602615346323,-11.901329934031464,-8.08475856265373,-1.0597856479085426,21.258345276879325,-16.737381796223453,13.07845062231035,-15.176234679376302,-20.159824811362636,16.227256425528704,-3.156043066076531,0.9922621244223498,-7.891052746447239,7.189024131719262,13.718651229619358,-5.099774445097151,27.350895767206772,0.3443563949303092,-7.6333332439892505,11.21375861282173,2.2317207565390795,1.4829216007143886,-2.675553839703211,-15.460123961200708,7.908376131637188,4.519521227804163,-0.26104911008719256,-6.116003479865864,5.0062610364533,0.1609638369183955,-7.699120056298718 PARAMETERS the parameters of the arguments in your function=0.14793206,0.23554253,0.23942723,0.37736514,0.46985096,0.45507910,0.47587387,0.54215042,0.65023246,0.12265400,0.13386633,0.24699632,0.35728471,0.32734440,0.36744060,0.41206731,0.52840113,0.22507163,0.28340231,0.40191476,0.34036292,0.38765113,0.40262109,0.50959110,0.14507431,0.24513329,0.24943681,0.29944994,0.34846052,0.47548652,0.15437548,0.15303349,0.24141877,0.24572214,0.38227046,0.25241096,0.32159147,0.33015009,0.45908219,0.12325800,0.13475260,0.24543985,0.22473502,0.27783004,0.14452999 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
tica1The COMBINE action with label tica1 calculates the following quantities:
 Quantity   
 Type   
 Description  
tica1
scalar
a linear compbination: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=pair1,pair2,pair3,pair4,pair5,pair6,pair7,pair8,pair9,pair10,pair11,pair12,pair13,pair14,pair15,pair16,pair17,pair18,pair19,pair20,pair21,pair22,pair23,pair24,pair25,pair26,pair27,pair28,pair29,pair30,pair31,pair32,pair33,pair34,pair35,pair36,pair37,pair38,pair39,pair40,pair41,pair42,pair43,pair44,pair45 COEFFICIENTS the coefficients of the arguments in your function=-1.0284232359442331,-0.11189619173402238,-5.041738294564907,1.7765576154735567,-3.268100290521192,-12.177517916388934,12.904229282608304,0.35442276782186133,-3.44487893762799,-6.440829566605922,7.700725644770633,2.290425263890155,2.4304564372058297,-3.2274523002278115,-19.7269113992782,14.306188155114919,6.946279136241224,1.9001838529944575,-15.349424064315645,4.311139778872364,24.252909954515342,-2.449699602066552,-11.449782346672992,-1.8317058894449605,13.798844007259968,-0.3939082727848911,-16.141031146494964,17.88225212212426,-3.0245513113682296,-7.179762607377906,-8.291730627590727,-3.7367159341939256,-6.474704047403058,9.398595486084506,8.699988730336177,14.439459790028495,-3.5494100566606,-2.691358017375163,-3.9075642682866016,15.689510454389845,-12.547731460317056,-2.6544839358652403,-0.7810877801495375,4.185327319758563,-0.7020828484440822 PARAMETERS the parameters of the arguments in your function=0.14793206,0.23554253,0.23942723,0.37736514,0.46985096,0.45507910,0.47587387,0.54215042,0.65023246,0.12265400,0.13386633,0.24699632,0.35728471,0.32734440,0.36744060,0.41206731,0.52840113,0.22507163,0.28340231,0.40191476,0.34036292,0.38765113,0.40262109,0.50959110,0.14507431,0.24513329,0.24943681,0.29944994,0.34846052,0.47548652,0.15437548,0.15303349,0.24141877,0.24572214,0.38227046,0.25241096,0.32159147,0.33015009,0.45908219,0.12325800,0.13475260,0.24543985,0.22473502,0.27783004,0.14452999 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
phiThe 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. 
opesThe OPES_METAD 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.nlker
scalar
number of kernels in the neighbor list
opes.nlsteps
scalar
number of steps from last neighbor list update: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
    ARGthe labels of the scalars on which the bias will act=tica0,tica1
    PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=20
    SIGMA the initial widths of the kernels=1.1051554159234913,0.4416132091381086
    STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=../STATE
    STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=../STATE
    NLIST use neighbor list for kernels summation, faster but experimental
    WALKERS_MPI switch on MPI version of multiple walkers
...
opes: OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action uses the defaults shown here. More details ...
    ARGthe labels of the scalars on which the bias will act=tica0,tica1
    PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=20
    SIGMA the initial widths of the kernels=1.1051554159234913,0.4416132091381086
    STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=../STATE
    STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=../STATE
    NLIST use neighbor list for kernels summation, faster but experimental
    WALKERS_MPI switch on MPI version of multiple walkers
 TEMP temperature=-1 COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=phi,psi,tica0,tica1,opes.* 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