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create ABF with weighted integration NAMD test
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‎namd/tests/library/010_bis_angle_dihedral_weighted/AutoDiff/test.colvars.out‎

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colvars: ----------------------------------------------------------------------
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colvars: Please cite Fiorin et al, Mol Phys 2013:
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colvars: https://doi.org/10.1080/00268976.2013.813594
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colvars: as well as all other papers listed below for individual features used.
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colvars: Summary of compile-time features available in this build:
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colvars: - C++ language version: 201703
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colvars: - Multiple replicas: enabled (replica number 1 of 1)
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colvars: - Lepton custom functions: available
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colvars: - Tcl interpreter: available
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colvars: Redefining the Tcl "cv" command to the new script interface.
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colvars: ----------------------------------------------------------------------
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colvars: Reading new configuration from file "test.in":
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colvars: # units = "" [default]
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colvars: # indexFile = "../Common/da.ndx"
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colvars: The following index groups are currently defined:
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colvars: Protein (104 atoms)
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colvars: Protein_noH (51 atoms)
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colvars: Protein_Backbone (40 atoms)
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colvars: Protein_C-alpha (10 atoms)
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colvars: RMSD_atoms (10 atoms)
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colvars: Protein_C-alpha_1_2 (2 atoms)
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colvars: Protein_C-alpha_9_10 (2 atoms)
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colvars: Protein_C-alpha_1 (1 atoms)
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colvars: group1 (4 atoms)
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colvars: Protein_C-alpha_2 (1 atoms)
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colvars: group2 (4 atoms)
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colvars: Protein_C-alpha_3 (1 atoms)
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colvars: group3 (4 atoms)
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colvars: Protein_C-alpha_4 (1 atoms)
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colvars: group4 (4 atoms)
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colvars: Protein_C-alpha_5 (1 atoms)
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colvars: group5 (4 atoms)
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colvars: Protein_C-alpha_6 (1 atoms)
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colvars: group6 (4 atoms)
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colvars: Protein_C-alpha_7 (1 atoms)
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colvars: group7 (4 atoms)
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colvars: Protein_C-alpha_8 (1 atoms)
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colvars: group8 (4 atoms)
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colvars: Protein_C-alpha_9 (1 atoms)
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colvars: group9 (4 atoms)
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colvars: Protein_C-alpha_10 (1 atoms)
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colvars: group10 (4 atoms)
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colvars: heavy_atoms (51 atoms)
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colvars: prot_N (10 atoms)
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colvars: prot_CA (10 atoms)
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colvars: prot_C (10 atoms)
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colvars: prot_O (10 atoms)
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colvars: # smp = "" [default]
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colvars: SMP parallelism is not set.
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colvars: Available SMP parallelism modes of this proxy are:
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colvars: - cvcs
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colvars: - inner_loop
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colvars: - none
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colvars: Set SMP parallelism to the preferred (default) mode to the proxy.
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colvars: SMP parallelism will be applied to Colvars components.
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colvars: - SMP parallelism: enabled (num. threads = 4)
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colvars: # colvarsTrajFrequency = 1
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colvars: # colvarsRestartFrequency = 0 [default]
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colvars: # scriptedColvarForces = off [default]
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colvars: # scriptingAfterBiases = off [default]
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colvars: # sourceTclFile = "" [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = "angle"
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colvars: Initializing a new "angle" component.
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colvars: # name = "" [default]
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # scalable = on [default]
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colvars: Initializing atom group "group1".
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colvars: # name = "" [default]
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colvars: # centerToOrigin = off [default]
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colvars: # centerToReference = off [default]
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colvars: # rotateToReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "Protein_C-alpha_1"
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableFitGradients = on [default]
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colvars: Enabling scalable calculation for group "group1".
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = -0.1.
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colvars: Initializing atom group "group2".
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colvars: # name = "" [default]
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colvars: # centerToOrigin = off [default]
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colvars: # centerToReference = off [default]
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colvars: # rotateToReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "Protein_C-alpha_2"
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableFitGradients = on [default]
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colvars: Enabling scalable calculation for group "group2".
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07.
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colvars: Initializing atom group "group3".
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colvars: # name = "" [default]
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colvars: # centerToOrigin = off [default]
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colvars: # centerToReference = off [default]
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colvars: # rotateToReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "Protein_C-alpha_3"
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableFitGradients = on [default]
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colvars: Enabling scalable calculation for group "group3".
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07.
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colvars: # oneSiteSystemForce = off [default]
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colvars: # oneSiteTotalForce = off [default]
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colvars: All components initialized.
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colvars: # timeStepFactor = 1 [default]
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colvars: # width = 6
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colvars: # lowerBoundary = 0
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colvars: # upperBoundary = 180
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colvars: # hardLowerBoundary = on [default]
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colvars: # hardUpperBoundary = on [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputTotalForce = on
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colvars: # outputAppliedForce = on
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colvars: # subtractAppliedForce = off [default]
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colvars: # runAve = off [default]
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colvars: # corrFunc = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = "dihedral"
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colvars: Initializing a new "dihedral" component.
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colvars: # name = "" [default]
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 360 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # scalable = on [default]
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colvars: Initializing atom group "group1".
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colvars: # name = "" [default]
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colvars: # centerToOrigin = off [default]
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colvars: # centerToReference = off [default]
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colvars: # rotateToReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "Protein_C-alpha_4"
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableFitGradients = on [default]
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colvars: Enabling scalable calculation for group "group1".
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group1" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07.
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colvars: Initializing atom group "group2".
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colvars: # name = "" [default]
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colvars: # centerToOrigin = off [default]
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colvars: # centerToReference = off [default]
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colvars: # rotateToReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "Protein_C-alpha_5"
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableFitGradients = on [default]
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colvars: Enabling scalable calculation for group "group2".
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group2" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07.
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colvars: Initializing atom group "group3".
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colvars: # name = "" [default]
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colvars: # centerToOrigin = off [default]
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colvars: # centerToReference = off [default]
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colvars: # rotateToReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "Protein_C-alpha_6"
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableFitGradients = on [default]
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colvars: Enabling scalable calculation for group "group3".
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group3" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07.
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colvars: Initializing atom group "group4".
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colvars: # name = "" [default]
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colvars: # centerToOrigin = off [default]
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colvars: # centerToReference = off [default]
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colvars: # rotateToReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "Protein_C-alpha_7"
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableFitGradients = on [default]
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colvars: Enabling scalable calculation for group "group4".
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group4" defined with 1 atoms requested: total mass = 12.011, total charge = 0.07.
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colvars: # oneSiteSystemForce = off [default]
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colvars: # oneSiteTotalForce = off [default]
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colvars: All components initialized.
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colvars: # timeStepFactor = 1 [default]
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colvars: # width = 6
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colvars: # lowerBoundary = 0
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colvars: # upperBoundary = 180
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colvars: # hardLowerBoundary = off [default]
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colvars: # hardUpperBoundary = on [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputTotalForce = on
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colvars: # outputAppliedForce = on
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colvars: # subtractAppliedForce = off [default]
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colvars: # runAve = off [default]
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colvars: # corrFunc = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables initialized, 2 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new "abf" instance.
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colvars: # name = "abf1" [default]
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colvars: # colvars = { angle, dihedral }
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colvars: # stepZeroData = off [default]
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colvars: # timeStepFactor = 1 [default]
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colvars: # outputEnergy = off [default]
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colvars: # outputFreq = 5
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colvars: # applyBias = on [default]
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colvars: # hideJacobian = off [default]
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colvars: Jacobian (geometric) forces will be included in reported free energy gradients.
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colvars: # fullSamples = 1
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colvars: # minSamples = 0 [default]
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colvars: # inputPrefix = [default]
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colvars: # historyFreq = 5
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colvars: # shared = off [default]
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colvars: # updateBias = on [default]
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colvars: # maxForce = [default]
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colvars: # integrate = on [default]
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colvars: 31 computation : 29
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colvars: Will perform weighted Poisson integrator using 1 threads.
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colvars: Finished ABF setup.
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables biases initialized, 1 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables module (re)initialized.
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colvars: ----------------------------------------------------------------------
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colvars: Updating NAMD interface:
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colvars: updating atomic data (0 atoms).
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colvars: updating group data (7 scalable groups, 7 atoms in total).
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colvars: updating grid object data (0 grid objects in total).
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colvars:
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colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
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colvars:
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colvars: - Colvars module:
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colvars: - Colvars-NAMD interface:
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colvars: - Optimal rotation via flexible fitting:
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colvars: - angle colvar component:
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colvars: - dihedral colvar component:
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colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
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colvars:
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colvars: - ABF colvar bias implementation:
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colvars: - Internal-forces free energy estimator:
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colvars: Henin2010 https://doi.org/10.1021/ct9004432
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colvars:
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colvars: - Poisson integration of 2D/3D free energy surfaces:
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colvars: Henin2021 https://doi.org/10.1021/acs.jctc.1c00593
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colvars:
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colvars: - NAMD engine:
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colvars: - Scalable center-of-mass computation (NAMD):
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colvars: Phillips2020 https://doi.org/10.1063/5.0014475
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colvars:
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colvars: updating target temperature (T = 300 K).
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colvars: Current simulation parameters: initial step = 0, integration timestep = 0.5
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colvars: Updating atomic parameters (masses, charges, etc).
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colvars: Re-initialized atom group for variable "angle":0/0. 1 atoms: total mass = 12.011, total charge = -0.1.
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colvars: Re-initialized atom group for variable "angle":0/1. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "angle":0/2. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "dihedral":0/0. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "dihedral":0/1. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "dihedral":0/2. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "dihedral":0/3. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: The final output state file will be "test.colvars.state".
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colvars: Updating NAMD interface:
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colvars: updating atomic data (0 atoms).
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colvars: updating group data (7 scalable groups, 7 atoms in total).
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colvars: updating grid object data (0 grid objects in total).
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colvars: updating target temperature (T = 300 K).
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colvars: Current simulation parameters: initial step = 0, integration timestep = 0.5
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colvars: Updating atomic parameters (masses, charges, etc).
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colvars: Re-initialized atom group for variable "angle":0/0. 1 atoms: total mass = 12.011, total charge = -0.1.
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colvars: Re-initialized atom group for variable "angle":0/1. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "angle":0/2. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "dihedral":0/0. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "dihedral":0/1. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "dihedral":0/2. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Re-initialized atom group for variable "dihedral":0/3. 1 atoms: total mass = 12.011, total charge = 0.07.
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colvars: Laplacian computation will be precomputed; precomputing will use 4.38616e-05 GB of memory.
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colvars: Integrated in 98 steps, error: 9.25651e-07
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colvars: Laplacian computation will be precomputed; precomputing will use 4.38616e-05 GB of memory.
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colvars: Integrated in 1 steps, error: 6.37713e-07
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colvars: Laplacian computation will be precomputed; precomputing will use 4.38616e-05 GB of memory.
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colvars: Integrated in 99 steps, error: 9.51457e-07
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colvars: Laplacian computation will be precomputed; precomputing will use 4.38616e-05 GB of memory.
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colvars: Integrated in 1 steps, error: 6.46878e-07
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colvars: Saving collective variables state to "test.colvars.state".

‎namd/tests/library/010_bis_angle_dihedral_weighted/AutoDiff/test.colvars.traj‎

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# step angle ft_angle fa_angle dihedral ft_dihedral fa_dihedral
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0 9.68498695196423e+01 0.00000000000000e+00 0.00000000000000e+00 4.86056572577460e+01 0.00000000000000e+00 0.00000000000000e+00
3+
1 9.68581311788645e+01 -1.84451708831773e-02 1.84451708831773e-02 4.84876896364246e+01 -2.26204233738403e-02 2.26204233738403e-02
4+
2 9.68825903830917e+01 -1.75928069494257e-02 2.72415743578902e-02 4.83727459141996e+01 1.09239386526320e-01 -3.19992698893195e-02
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3 9.69105533161851e+01 -3.36465334818317e-02 3.84570855185007e-02 4.82565768693385e+01 1.87476845825582e-01 -9.44915518311800e-02
6+
4 9.69406101257451e+01 -8.90986866663619e-02 6.07317571850912e-02 4.81501282214520e+01 2.91829502654486e-01 -1.67448927494802e-01
7+
5 9.69674902853217e+01 -1.44712759388153e-01 8.96743090627219e-02 4.80499450162547e+01 4.19420612850750e-01 -2.51333050064952e-01
8+
6 9.69953149267565e+01 -1.91014192347198e-01 0.00000000000000e+00 4.79483470270909e+01 5.72126050345695e-01 0.00000000000000e+00
9+
7 9.70261917919329e+01 -3.39026775359721e-01 3.39026775359721e-01 4.78551169384050e+01 1.09938746010352e+00 -1.09938746010352e+00
10+
8 9.70529963144370e+01 -4.61821781835123e-02 3.62117864451477e-01 4.77722438820884e+01 2.55842716309053e-01 -1.22730881825804e+00
11+
9 9.70984141114596e+01 -2.94041075882320e-02 3.71919233647555e-01 4.76919701530931e+01 3.67640478945811e-01 -1.34985564457331e+00
12+
10 9.71572414999404e+01 -5.65433882803053e-02 3.86055080717631e-01 4.76248133822394e+01 4.86844972233637e-01 -1.47156688763172e+00

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