Bicyclohexane.world File Reference

Detailed Description

[Introduction] [Process] [Statistics] [Results]

Introduction

This benchmark illustrates CUIK's ability on dealing with multi-loop linkages or molecules. We refer here to interconnected loops where the motion of any loop influences the motion of the others, so that the analysis of the overall conformational space is irreducible to the analysis of the individual loop spaces.

Process

This example is treated following this steps (from the main CuikSuite folder):

  • Generate the equations: Execute
  • Solve the positional analysis problem: Execute
    • bin/cuik examples/Cycloalkanes/Bicyclohexane
  • Sort the solutions:
  • Animate the solutions (the flexible and the isolated):
    • scripts/cuikplayer examples/Bicycloalkanes/Cyclohexane examples/Cycloalkanes/Bicyclohexane_1
    • scripts/cuikplayer examples/Bicycloalkanes/Cyclohexane examples/Cycloalkanes/Bicyclohexane_isol
  • Plot and visualize the configuration space (you will see the one-dim solution and the isolated small boxes):
    • bin/cuikplot3d examples/Cycloalkanes/Bicyclohexane_1 9 17 37 0 bc6_1.cgl
    • bin/cuikplot3d examples/Cycloalkanes/Bicyclohexane_isol 9 17 37 0.025 bc6_isol.cgl
    • geomview bc6_1.gcl bc6_isol.gcl

Statistics

Characteristics of the problems:

Nr. of loops 2
Nr. of links 10
Nr. of joints 12
Nr. of equations (in the simplified system) 49
Nr. of variables (in the simplified system) 44

Here you have the statistics about the execution (on an Intel Core i7 at 2.9 Ghz).

Nr. of empty boxes 5055
Nr. of solution boxes 374
Solver time (s) 2500

Results

Conformational space of the bicylohexane. The red boxes are the (magnifed) isolated solutions.

Definition in file Bicyclohexane.world.