crank and reptation moves, no energy func

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@1 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
added vdw energy function

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@2 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
actual version 2

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@3 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
small fix for crankshaft move

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@4 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
added accept or reject to energy function

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@5 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
working markov chain of states by fixing issue with copy/deep copy

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@6 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
added bending potential to energy function

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@7 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
edited for random angle crankshaft move

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@8 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
fix bug in crankshaft move

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@9 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
added torsional move, fixed writepdb, added plot

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@10 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
very minor changes (plot title and total moves variable)

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@11 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
now outputs to one pdb file

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@12 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
Random coil calculation

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@13 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
added torsional energy calculation

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@14 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
added new Go-model simulation files and random coil test files

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@15 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
updated for new protein 2LFL.pdb

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@16 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
split up crank.py to moveset,writetopdb,energyfunc

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@17 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
implemented GO-like  model, completed energyfunc and updated simulateGO

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@18 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
removed obsolete files

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@19 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3
added axis torsion move, added repulsive radius calculation, small changes to torsion and ljenergy

git-svn-id: svn://fold3.che.virginia.edu/proteinmontecarlo@20 2b46cb21-ebdf-45b3-a131-b05a2c4c95c3