Implement reflecting boundary conditions for metadynamics bias

namd/tests/library/000_distance-grid_metadynamics-reflection/AutoDiff/test.colvars.out

@@ -0,0 +1,207 @@
+colvars: ----------------------------------------------------------------------
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:   https://doi.org/10.1080/00268976.2013.813594
+colvars: as well as all other papers listed below for individual features used.
+colvars: SMP parallelism is enabled (num threads = 4).
+colvars: This version was built with the C++11 standard or higher.
+colvars: Redefining the Tcl "cv" command to the new script interface.
+colvars: The restart output state file will be "test.tmp.colvars.state".
+colvars: The final output state file will be "test.colvars.state".
+colvars: ----------------------------------------------------------------------
+colvars: Reading new configuration from file "test.in":
+colvars: # units = "" [default]
+colvars: # indexFile = "index.ndx"
+colvars: The following index groups are currently defined:
+colvars:   Protein (104 atoms)
+colvars:   Protein_noH (51 atoms)
+colvars:   Protein_Backbone (40 atoms)
+colvars:   Protein_C-alpha (10 atoms)
+colvars:   RMSD_atoms (10 atoms)
+colvars:   Protein_C-alpha_1_2 (2 atoms)
+colvars:   Protein_C-alpha_9_10 (2 atoms)
+colvars:   Protein_C-alpha_1 (1 atoms)
+colvars:   group1 (4 atoms)
+colvars:   Protein_C-alpha_2 (1 atoms)
+colvars:   group2 (4 atoms)
+colvars:   Protein_C-alpha_3 (1 atoms)
+colvars:   group3 (4 atoms)
+colvars:   Protein_C-alpha_4 (1 atoms)
+colvars:   group4 (4 atoms)
+colvars:   Protein_C-alpha_5 (1 atoms)
+colvars:   group5 (4 atoms)
+colvars:   Protein_C-alpha_6 (1 atoms)
+colvars:   group6 (4 atoms)
+colvars:   Protein_C-alpha_7 (1 atoms)
+colvars:   group7 (4 atoms)
+colvars:   Protein_C-alpha_8 (1 atoms)
+colvars:   group8 (4 atoms)
+colvars:   Protein_C-alpha_9 (1 atoms)
+colvars:   group9 (4 atoms)
+colvars:   Protein_C-alpha_10 (1 atoms)
+colvars:   group10 (4 atoms)
+colvars:   heavy_atoms (51 atoms)
+colvars: # smp = on [default]
+colvars: # colvarsTrajFrequency = 1
+colvars: # colvarsRestartFrequency = 10
+colvars: # scriptedColvarForces = off [default]
+colvars: # scriptingAfterBiases = off [default]
+colvars: # sourceTclFile = "" [default]
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new collective variable.
+colvars:   # name = "one"
+colvars:   Initializing a new "distance" component.
+colvars:   # name = "" [default]
+colvars:   # componentCoeff = 1 [default]
+colvars:   # componentExp = 1 [default]
+colvars:   # period = 0 [default]
+colvars:   # wrapAround = 0 [default]
+colvars:   # forceNoPBC = off [default]
+colvars:   # scalable = on [default]
+colvars:     Initializing atom group "group1".
+colvars:     # name = "" [default]
+colvars:     # centerToOrigin = off [default]
+colvars:     # centerToReference = off [default]
+colvars:     # rotateToReference = off [default]
+colvars:     # atomsOfGroup = "" [default]
+colvars:     # indexGroup = "group1"
+colvars:     # psfSegID =  [default]
+colvars:     # atomsFile = "" [default]
+colvars:     # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:     # enableFitGradients = on [default]
+colvars:     Enabling scalable calculation for group "group1".
+colvars:     # printAtomIDs = off [default]
+colvars:     Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72.
+colvars:     Initializing atom group "group2".
+colvars:     # name = "" [default]
+colvars:     # centerToOrigin = off [default]
+colvars:     # centerToReference = off [default]
+colvars:     # rotateToReference = off [default]
+colvars:     # atomsOfGroup = "" [default]
+colvars:     # indexGroup = "group2"
+colvars:     # psfSegID =  [default]
+colvars:     # atomsFile = "" [default]
+colvars:     # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:     # enableFitGradients = on [default]
+colvars:     Enabling scalable calculation for group "group2".
+colvars:     # printAtomIDs = off [default]
+colvars:     Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4.
+colvars:   # oneSiteSystemForce = off [default]
+colvars:   # oneSiteTotalForce = off [default]
+colvars:   All components initialized.
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # width = 0.5
+colvars:   # lowerBoundary = 3.2
+colvars:   # upperBoundary = 10.2
+colvars:   # hardLowerBoundary = on
+colvars:   # hardUpperBoundary = on
+colvars:   # expandBoundaries = off [default]
+colvars:   # extendedLagrangian = off [default]
+colvars:   # outputValue = on [default]
+colvars:   # outputVelocity = off [default]
+colvars:   # outputTotalForce = off [default]
+colvars:   # outputAppliedForce = on
+colvars:   # subtractAppliedForce = off [default]
+colvars:   # runAve = off [default]
+colvars:   # corrFunc = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables initialized, 1 in total.
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "harmonicwalls" instance.
+colvars:   # name = "wall_one"
+colvars:   # colvars = { one }
+colvars:   # stepZeroData = off [default]
+colvars:   # outputEnergy = off [default]
+colvars:   # outputFreq = 10 [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
+colvars:   # forceConstant = 1
+colvars:   # decoupling = off [default]
+colvars:   # targetForceConstant = -1 [default]
+colvars:   # lowerWalls = { 3.2 }
+colvars:   # upperWalls = { 10.2 }
+colvars:   # lowerWallConstant = 1 [default]
+colvars:   # upperWallConstant = 1 [default]
+colvars:   The lower wall force constant for colvar "one" will be rescaled to 4 according to the specified width (0.5).
+colvars:   The upper wall force constant for colvar "one" will be rescaled to 4 according to the specified width (0.5).
+colvars: ----------------------------------------------------------------------
+colvars:   Initializing a new "metadynamics" instance.
+colvars:   # name = "metadynamics1" [default]
+colvars:   # colvars = { one }
+colvars:   # stepZeroData = off [default]
+colvars:   # outputEnergy = off [default]
+colvars:   # outputFreq = 10 [default]
+colvars:   # timeStepFactor = 1 [default]
+colvars:   # writeTISamples = off [default]
+colvars:   # writeTIPMF = off [default]
+colvars:   # hillWeight = 0.001
+colvars:   # newHillFrequency = 10
+colvars:   # gaussianSigmas =  [default]
+colvars:   # hillWidth = 1.25331
+colvars:   Half-widths of the Gaussian hills (sigma's):
+colvars:   one: 0.313329
+colvars:   # multipleReplicas = off [default]
+colvars:   # useGrids = on [default]
+colvars:   # gridsUpdateFrequency = 10 [default]
+colvars:   # rebinGrids = off [default]
+colvars:   # writeFreeEnergyFile = on [default]
+colvars:   # keepHills = off [default]
+colvars:   # keepFreeEnergyFiles = off [default]
+colvars:   # writeHillsTrajectory = off [default]
+colvars:   # wellTempered = off [default]
+colvars:   # biasTemperature = -1 [default]
+colvars:   # useHillsReflection = on
+colvars:   # reflectionRange = 6 [default]
+colvars:   Reflection range is 6.
+colvars:   # reflectionLowLimitUseCVs =  [default]
+colvars:   Using all non-periodic variables for lower limits of reflection 
+colvars:   # reflectionUpLimitUseCVs =  [default]
+colvars:   Using all non-periodic variables for upper limits of reflection 
+colvars:   # reflectionLowLimit = { 3.2 } [default]
+colvars:   Reflection condition is applied on a lower limit for CV 0.
+colvars:   Reflection condition lower limit for this CV is 3.2.
+colvars:   # reflectionUpLimit = { 10.2 } [default]
+colvars:   Reflection condition is applied on an upper limit for CV 0.
+colvars:   Reflection condition upper limit for this CV is 10.2.
+colvars:   # ebMeta = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 2 in total.
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables module (re)initialized.
+colvars: ----------------------------------------------------------------------
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (2 scalable groups, 8 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: 
+colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:
+colvars: 
+colvars: - Colvars module:
+colvars: - Colvars-NAMD interface:
+colvars: - Metadynamics colvar bias implementation:
+colvars: - Optimal rotation via flexible fitting:
+colvars: - distance colvar component:
+colvars: - harmonicWalls colvar bias implementation:
+colvars:   Fiorin2013 https://doi.org/10.1080/00268976.2013.813594
+colvars: 
+colvars: - NAMD engine:
+colvars: - Scalable center-of-mass computation (NAMD):
+colvars:   Phillips2020 https://doi.org/10.1063/5.0014475
+colvars: 
+colvars: updating target temperature (T = 0 K).
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (2 scalable groups, 8 atoms in total).
+colvars: updating grid object data (0 grid objects in total).
+colvars: updating target temperature (T = 0 K).
+colvars: Current simulation parameters: initial step = 0, integration timestep = 1
+colvars: Updating atomic parameters (masses, charges, etc).
+colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72.
+colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4.
+colvars: The restart output state file will be "test.tmp.colvars.state".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
+colvars: Saving collective variables state to "test.tmp.colvars.state".
+colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj".
+colvars: Saving collective variables state to "test.tmp.colvars.state".
+colvars: Saving collective variables state to "test.colvars.state".

namd/tests/library/000_distance-grid_metadynamics-reflection/AutoDiff/test.colvars.state.stripped

@@ -0,0 +1,52 @@
+configuration {
+  step           20
+  dt 1.000000e+00
+}
+
+colvar {
+  name one
+  x       3.2168853380692
+}
+
+restraint {
+  configuration {
+step 20
+name wall_one
+  }
+}
+
+metadynamics {
+  configuration {
+step 20
+name metadynamics1
+  }
+
+hills_energy
+grid_parameters {
+  n_colvars 1
+  lower_boundaries  3.2
+  upper_boundaries  10.2
+  widths  0.5
+  sizes  14
+}
+ 2.90793197471122e-03 2.29589040998682e-04 1.43098718458920e-06
+ 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 0.00000000000000e+00 0.00000000000000e+00
+
+hills_energy_gradients
+grid_parameters {
+  n_colvars 1
+  lower_boundaries  3.2
+  upper_boundaries  10.2
+  widths  0.5
+  sizes  14
+}
+ -7.38291182480299e-03 -1.74872845262777e-03 -1.81663860935017e-05
+ 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 0.00000000000000e+00 0.00000000000000e+00
+}
+

namd/tests/library/000_distance-grid_metadynamics-reflection/AutoDiff/test.colvars.traj

@@ -0,0 +1,22 @@
+# step         one                   fa_one                 
+           0    3.20554673468334e+00  0.00000000000000e+00  
+           1    3.20437148316484e+00  0.00000000000000e+00  
+           2    3.20384028588952e+00  0.00000000000000e+00  
+           3    3.20396721186862e+00  0.00000000000000e+00  
+           4    3.20472817286016e+00  0.00000000000000e+00  
+           5    3.20606308065050e+00  0.00000000000000e+00  
+           6    3.20787989000757e+00  0.00000000000000e+00  
+           7    3.21005997940810e+00  0.00000000000000e+00  
+           8    3.21246460651160e+00  0.00000000000000e+00  
+           9    3.21494247383722e+00  0.00000000000000e+00  
+          10    3.21733851230199e+00  3.69111079117202e-03  
+          11    3.21950373044117e+00  3.69111079117202e-03  
+          12    3.22130516783262e+00  3.69111079117202e-03  
+          13    3.22263513141286e+00  3.69111079117202e-03  
+          14    3.22341825276891e+00  3.69111079117202e-03  
+          15    3.22361556235479e+00  3.69111079117202e-03  
+          16    3.22322531690825e+00  3.69111079117202e-03  
+          17    3.22228092687886e+00  3.69111079117202e-03  
+          18    3.22084669842434e+00  3.69111079117202e-03  
+          19    3.21901213410055e+00  3.69111079117202e-03  
+          20    3.21688533806922e+00  7.38291182480299e-03  

namd/tests/library/000_distance-grid_metadynamics-reflection/AutoDiff/test.pmf

@@ -0,0 +1,17 @@
+# 1
+#  3.20000000000000e+00  5.00000000000000e-01         14  0
+
+  3.45000000000000e+00  -0.00000000000000e+00
+  3.95000000000000e+00   2.67834293371254e-03
+  4.45000000000000e+00   2.90650098752663e-03
+  4.95000000000000e+00   2.90793197471122e-03
+  5.45000000000000e+00   2.90793197471122e-03
+  5.95000000000000e+00   2.90793197471122e-03
+  6.45000000000000e+00   2.90793197471122e-03
+  6.95000000000000e+00   2.90793197471122e-03
+  7.45000000000000e+00   2.90793197471122e-03
+  7.95000000000000e+00   2.90793197471122e-03
+  8.45000000000000e+00   2.90793197471122e-03
+  8.95000000000000e+00   2.90793197471122e-03
+  9.45000000000000e+00   2.90793197471122e-03
+  9.95000000000000e+00   2.90793197471122e-03