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colvarsTrajFrequency 50 
colvarsRestartFrequency 50000
colvar {
  name theta

  width 1
  lowerboundary 20
  upperboundary 160
  lowerWallConstant 10
  upperWallConstant 10

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00233         cvm::fatal_error ("Error: the atom group \""+
00234                           std::string (key)+"\" has already a reference group "
00235                           "for the rototranslational fit, which was communicated by the "
00236                           "colvar component.  You should not use refPositionsGroup "
00237                           "in this case.\n");

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CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
ATOM      1  N   ALA P   1       0.201   1.256 -26.667  1.00  1.00      P    N
ATOM      2  HT1 ALA P   1       0.493   1.913 -27.418  0.00  0.00      P    H
ATOM      3  HT2 ALA P   1       0.074   0.305 -27.067  0.00  0.00      P    H
ATOM      4  HT3 ALA P   1       0.931   1.227 -25.927  0.00  0.00      P    H
ATOM      5  CA  ALA P   1      -1.080   1.718 -26.078  1.00  1.00      P    C
ATOM      6  HA  ALA P   1      -0.902   2.700 -25.665  1.00  0.00      P    H
ATOM      7  CB  ALA P   1      -2.173   1.787 -27.166  1.00  0.00      P    C
ATOM      8  HB1 ALA P   1      -3.135   2.133 -26.730  1.00  0.00      P    H
ATOM      9  HB2 ALA P   1      -1.878   2.509 -27.957  1.00  0.00      P    H

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CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1           1
ATOM      1  N   R1A P  18       0.996  -1.268  -0.798  1.00  1.00      P    N
ATOM      2  CA  R1A P  18       2.046  -0.803   0.079  1.00  1.00      P    C
ATOM      3  CB  R1A P  18       3.163  -0.061  -0.699  1.00  0.00      P    C
ATOM      4  C   R1A P  18       1.494   0.121   1.139  1.00  1.00      P    C
ATOM      5  O   R1A P  18       1.885   0.042   2.301  1.00  1.00      P    O
END

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    (*Original implementation*)
    MakeInPeriodicCellOrig = 
      Compile[{x, cellwidth}, 
       First@Sort[{x, x - cellwidth, x + cellwidth}, 
         Abs[#1] < Abs[#2] &], {{Sort[_], _Real}}, 
       CompilationOptions -> {"ExpressionOptimization" -> True, 
         "InlineCompiledFunctions" -> True, 
         "InlineExternalDefinitions" -> True},
           RuntimeAttributes -> {Listable},
           "RuntimeOptions" -> "Speed"

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(* Produces compiled code for the Nelder-Mead algorithm with the objective function inlined. *)
(* The objective function takes the form F[parametersToOptimize..,constantParameters] *)
NelderMeadMinimize`Dump`CompiledNelderMead[
   objectiveFunction_Function | objectiveFunction_CompiledFunction, vars : {__Symbol}, const: {__Symbol},
   opts : OptionsPattern[NelderMeadMinimize`Dump`CompiledNelderMead]
  ] :=
  NelderMeadMinimize`Dump`CompiledNelderMead[
    objectiveFunction, vars, const
    opts
   ] =

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