Implement reflecting boundary conditions for metadynamics bias

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

@@ -0,0 +1,157 @@
+colvars: ----------------------------------------------------------------------
+colvars: Please cite Fiorin et al, Mol Phys 2013:
+colvars:  https://dx.doi.org/10.1080/00268976.2013.813594
+colvars: in any publication based on this calculation.
+colvars: SMP parallelism is enabled; if needed, use "smp off" to override this.
+colvars: This version was built with the C++11 standard or higher.
+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: ----------------------------------------------------------------------
+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:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "group1"
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [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:       # centerReference = off [default]
+colvars:       # rotateReference = off [default]
+colvars:       # atomsOfGroup = "" [default]
+colvars:       # indexGroup = "group2"
+colvars:       # psfSegID =  [default]
+colvars:       # atomsFile = "" [default]
+colvars:       # dummyAtom = ( 0 , 0 , 0 ) [default]
+colvars:       # enableForces = on [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 = 0 [default]
+colvars:   # upperBoundary = 10
+colvars:   # hardLowerBoundary = on [default]
+colvars:   # hardUpperBoundary = off [default]
+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 "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:   # ebMeta = off [default]
+colvars: ----------------------------------------------------------------------
+colvars: Collective variables biases initialized, 1 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: 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: The final output state file will be "test.colvars.state".
+colvars: Opening trajectory file "test.colvars.traj".
+colvars: Redefining the Tcl "cv" command to the new script interface.
+colvars: Updating NAMD interface:
+colvars: updating atomic data (0 atoms).
+colvars: updating group data (2 scalable groups, 8 atoms in total).
+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: The final output state file will be "test.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 +1,47 @@
+configuration {
+  step           20
+  dt 1.000000e+00
+}
+
+colvar {
+  name one
+  x  3.21688278597333e+00
+}
+
+metadynamics {
+  configuration {
+    step 20
+    name metadynamics1
+  }
+  hills_energy
+grid_parameters {
+  n_colvars 1
+  lower_boundaries  0.00000000000000e+00
+  upper_boundaries  1.00000000000000e+01
+  widths  5.00000000000000e-01
+  sizes  20
+}
+ 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 3.46920492770083e-08 1.70721010112539e-05 6.58298335288197e-04
+ 1.98901157291202e-03 4.70902104436801e-04 8.73580076380761e-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  0.00000000000000e+00
+  upper_boundaries  1.00000000000000e+01
+  widths  5.00000000000000e-01
+  sizes  20
+}
+ 0.00000000000000e+00 0.00000000000000e+00 0.00000000000000e+00
+ 5.18433073974142e-07 1.68175610579987e-04 3.13214890940428e-03
+ -6.66334787942696e-04 -2.55603942784152e-03 -9.19086519769792e-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    3.20437148316546e+00  0.00000000000000e+00 
+           2    3.20384028589204e+00  0.00000000000000e+00 
+           3    3.20396721187433e+00  0.00000000000000e+00 
+           4    3.20472817287036e+00  0.00000000000000e+00 
+           5    3.20606308066645e+00  0.00000000000000e+00 
+           6    3.20787989003051e+00  0.00000000000000e+00 
+           7    3.21005997943917e+00  0.00000000000000e+00 
+           8    3.21246460655188e+00  0.00000000000000e+00 
+           9    3.21494247388772e+00  0.00000000000000e+00 
+          10    3.21733851236362e+00  3.30884583259955e-04 
+          11    3.21950367891521e+00  3.30884583259955e-04 
+          12    3.22130501376020e+00  3.30884583259955e-04 
+          13    3.22263482513293e+00  3.30884583259955e-04 
+          14    3.22341774651982e+00  3.30884583259955e-04 
+          15    3.22361481079113e+00  3.30884583259955e-04 
+          16    3.22322427751010e+00  3.30884583259955e-04 
+          17    3.22227956023865e+00  3.30884583259955e-04 
+          18    3.22084496840419e+00  3.30884583259955e-04 
+          19    3.21901000786075e+00  3.30884583259955e-04 
+          20    3.21688278597333e+00  6.66334787942696e-04 

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

@@ -0,0 +1,23 @@
+# 1
+#  0.00000000000000e+00  5.00000000000000e-01         20  0
+
+  2.50000000000000e-01   1.98901157291202e-03
+  7.50000000000000e-01   1.98901157291202e-03
+  1.25000000000000e+00   1.98901157291202e-03
+  1.75000000000000e+00   1.98897688086274e-03
+  2.25000000000000e+00   1.97193947190077e-03
+  2.75000000000000e+00   1.33071323762382e-03
+  3.25000000000000e+00  -0.00000000000000e+00
+  3.75000000000000e+00   1.51810946847522e-03
+  4.25000000000000e+00   1.98027577214821e-03
+  4.75000000000000e+00   1.98901157291202e-03
+  5.25000000000000e+00   1.98901157291202e-03
+  5.75000000000000e+00   1.98901157291202e-03
+  6.25000000000000e+00   1.98901157291202e-03
+  6.75000000000000e+00   1.98901157291202e-03
+  7.25000000000000e+00   1.98901157291202e-03
+  7.75000000000000e+00   1.98901157291202e-03
+  8.25000000000000e+00   1.98901157291202e-03
+  8.75000000000000e+00   1.98901157291202e-03
+  9.25000000000000e+00   1.98901157291202e-03
+  9.75000000000000e+00   1.98901157291202e-03