Moved examples

Moved the examples out of the package and up into the top level, this should be beneficial for preparing packages for release.
HECBioSim · Sep 8, 2016 · 600d56b · 600d56b
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diff --git a/...gbowExamples/CondorSubmission/condor_desc → Examples/CondorSubmission/condor_desc b/...gbowExamples/CondorSubmission/condor_desc → Examples/CondorSubmission/condor_desc
diff --git a/...ngbowExamples/CondorSubmission/example.in → Examples/CondorSubmission/example.in b/...ngbowExamples/CondorSubmission/example.in → Examples/CondorSubmission/example.in
diff --git a/...gbowExamples/CondorSubmission/example.min → Examples/CondorSubmission/example.min b/...gbowExamples/CondorSubmission/example.min → Examples/CondorSubmission/example.min
diff --git a/...gbowExamples/CondorSubmission/example.top → Examples/CondorSubmission/example.top b/...gbowExamples/CondorSubmission/example.top → Examples/CondorSubmission/example.top
diff --git a/...es/MultipleJobs/MultipleJobTypes/job.conf → ...es/MultipleJobs/MultipleJobTypes/job.conf b/...es/MultipleJobs/MultipleJobTypes/job.conf → ...es/MultipleJobs/MultipleJobTypes/job.conf
diff --git a/...bs/MultipleJobTypes/replicate/example.rst → ...bs/MultipleJobTypes/replicate/example.rst b/...bs/MultipleJobTypes/replicate/example.rst → ...bs/MultipleJobTypes/replicate/example.rst
diff --git a/...bs/MultipleJobTypes/replicate/example.top → ...bs/MultipleJobTypes/replicate/example.top b/...bs/MultipleJobTypes/replicate/example.top → ...bs/MultipleJobTypes/replicate/example.top
diff --git a/...ultipleJobTypes/replicate/rep1/example.in → ...ultipleJobTypes/replicate/rep1/example.in b/...ultipleJobTypes/replicate/rep1/example.in → ...ultipleJobTypes/replicate/rep1/example.in
diff --git a/...ultipleJobTypes/replicate/rep2/example.in → ...ultipleJobTypes/replicate/rep2/example.in b/...ultipleJobTypes/replicate/rep2/example.in → ...ultipleJobTypes/replicate/rep2/example.in
diff --git a/...ultipleJobTypes/replicate/rep3/example.in → ...ultipleJobTypes/replicate/rep3/example.in b/...ultipleJobTypes/replicate/rep3/example.in → ...ultipleJobTypes/replicate/rep3/example.in
diff --git a/...ultipleJobTypes/replicate/rep4/example.in → ...ultipleJobTypes/replicate/rep4/example.in b/...ultipleJobTypes/replicate/rep4/example.in → ...ultipleJobTypes/replicate/rep4/example.in
diff --git a/...ultipleJobTypes/replicate/rep5/example.in → ...ultipleJobTypes/replicate/rep5/example.in b/...ultipleJobTypes/replicate/rep5/example.in → ...ultipleJobTypes/replicate/rep5/example.in
diff --git a/...leJobs/MultipleJobTypes/single/example.in → ...leJobs/MultipleJobTypes/single/example.in b/...leJobs/MultipleJobTypes/single/example.in → ...leJobs/MultipleJobTypes/single/example.in
diff --git a/...eJobs/MultipleJobTypes/single/example.rst → ...eJobs/MultipleJobTypes/single/example.rst b/...eJobs/MultipleJobTypes/single/example.rst → ...eJobs/MultipleJobTypes/single/example.rst
diff --git a/...eJobs/MultipleJobTypes/single/example.top → ...eJobs/MultipleJobTypes/single/example.top b/...eJobs/MultipleJobTypes/single/example.top → ...eJobs/MultipleJobTypes/single/example.top
diff --git a/...obsDifferentApplications/amber/example.in → ...obsDifferentApplications/amber/example.in b/...obsDifferentApplications/amber/example.in → ...obsDifferentApplications/amber/example.in
diff --git a/...bsDifferentApplications/amber/example.rst → ...bsDifferentApplications/amber/example.rst b/...bsDifferentApplications/amber/example.rst → ...bsDifferentApplications/amber/example.rst
diff --git a/...bsDifferentApplications/amber/example.top → ...bsDifferentApplications/amber/example.top b/...bsDifferentApplications/amber/example.top → ...bsDifferentApplications/amber/example.top
diff --git a/...fferentApplications/gromacs_d/example.tpr → ...fferentApplications/gromacs_d/example.tpr b/...fferentApplications/gromacs_d/example.tpr → ...fferentApplications/gromacs_d/example.tpr
diff --git a/...fferentApplications/gromacs_s/example.tpr → ...fferentApplications/gromacs_s/example.tpr b/...fferentApplications/gromacs_s/example.tpr → ...fferentApplications/gromacs_s/example.tpr
diff --git a/...ultipleJobsDifferentApplications/job.conf → ...ultipleJobsDifferentApplications/job.conf b/...ultipleJobsDifferentApplications/job.conf → ...ultipleJobsDifferentApplications/job.conf
diff --git a/...DifferentApplications/lammps/example.data → ...DifferentApplications/lammps/example.data b/...DifferentApplications/lammps/example.data → ...DifferentApplications/lammps/example.data
diff --git a/...bsDifferentApplications/lammps/example.in → ...bsDifferentApplications/lammps/example.in b/...bsDifferentApplications/lammps/example.in → ...bsDifferentApplications/lammps/example.in
diff --git a/...JobsDifferentApplications/namd/example.in → ...JobsDifferentApplications/namd/example.in b/...JobsDifferentApplications/namd/example.in → ...JobsDifferentApplications/namd/example.in
diff --git a/...pplications/namd/par_all27_prot_lipid.prm → ...pplications/namd/par_all27_prot_lipid.prm b/...pplications/namd/par_all27_prot_lipid.prm → ...pplications/namd/par_all27_prot_lipid.prm
diff --git a/...obsDifferentApplications/namd/relres.coor → ...obsDifferentApplications/namd/relres.coor b/...obsDifferentApplications/namd/relres.coor → ...obsDifferentApplications/namd/relres.coor
diff --git a/...JobsDifferentApplications/namd/relres.vel → ...JobsDifferentApplications/namd/relres.vel b/...JobsDifferentApplications/namd/relres.vel → ...JobsDifferentApplications/namd/relres.vel
diff --git a/...JobsDifferentApplications/namd/relres.xsc → ...JobsDifferentApplications/namd/relres.xsc b/...JobsDifferentApplications/namd/relres.xsc → ...JobsDifferentApplications/namd/relres.xsc
diff --git a/...bsDifferentApplications/namd/solvated.pdb → ...bsDifferentApplications/namd/solvated.pdb b/...bsDifferentApplications/namd/solvated.pdb → ...bsDifferentApplications/namd/solvated.pdb
diff --git a/...bsDifferentApplications/namd/solvated.psf → ...bsDifferentApplications/namd/solvated.psf b/...bsDifferentApplications/namd/solvated.psf → ...bsDifferentApplications/namd/solvated.psf
diff --git a/...ngbowExamples/QuickStart/Amber/example.in → Examples/QuickStart/Amber/example.in b/...ngbowExamples/QuickStart/Amber/example.in → Examples/QuickStart/Amber/example.in
diff --git a/...gbowExamples/QuickStart/Amber/example.min → Examples/QuickStart/Amber/example.min b/...gbowExamples/QuickStart/Amber/example.min → Examples/QuickStart/Amber/example.min
diff --git a/...gbowExamples/QuickStart/Amber/example.top → Examples/QuickStart/Amber/example.top b/...gbowExamples/QuickStart/Amber/example.top → Examples/QuickStart/Amber/example.top
diff --git a/...bowExamples/QuickStart/CHARMM/example.crd → Examples/QuickStart/CHARMM/example.crd b/...bowExamples/QuickStart/CHARMM/example.crd → Examples/QuickStart/CHARMM/example.crd
diff --git a/...bowExamples/QuickStart/CHARMM/example.inp → Examples/QuickStart/CHARMM/example.inp b/...bowExamples/QuickStart/CHARMM/example.inp → Examples/QuickStart/CHARMM/example.inp
diff --git a/...bowExamples/QuickStart/CHARMM/example.psf → Examples/QuickStart/CHARMM/example.psf b/...bowExamples/QuickStart/CHARMM/example.psf → Examples/QuickStart/CHARMM/example.psf
diff --git a/...bowExamples/QuickStart/CHARMM/example.rst → Examples/QuickStart/CHARMM/example.rst b/...bowExamples/QuickStart/CHARMM/example.rst → Examples/QuickStart/CHARMM/example.rst
diff --git a/...uickStart/CHARMM/par_all27_prot_lipid.prm → ...uickStart/CHARMM/par_all27_prot_lipid.prm b/...uickStart/CHARMM/par_all27_prot_lipid.prm → ...uickStart/CHARMM/par_all27_prot_lipid.prm
diff --git a/...uickStart/CHARMM/top_all27_prot_lipid.rtf → ...uickStart/CHARMM/top_all27_prot_lipid.rtf b/...uickStart/CHARMM/top_all27_prot_lipid.rtf → ...uickStart/CHARMM/top_all27_prot_lipid.rtf
diff --git a/...ngbowExamples/QuickStart/Gromacs/3NIR.top → Examples/QuickStart/Gromacs/3NIR.top b/...ngbowExamples/QuickStart/Gromacs/3NIR.top → Examples/QuickStart/Gromacs/3NIR.top
diff --git a/...wExamples/QuickStart/Gromacs/_example.mdp → Examples/QuickStart/Gromacs/_example.mdp b/...wExamples/QuickStart/Gromacs/_example.mdp → Examples/QuickStart/Gromacs/_example.mdp
diff --git a/...owExamples/QuickStart/Gromacs/example.tpr → Examples/QuickStart/Gromacs/example.tpr b/...owExamples/QuickStart/Gromacs/example.tpr → Examples/QuickStart/Gromacs/example.tpr
diff --git a/...owExamples/QuickStart/LAMMPS/example.data → Examples/QuickStart/LAMMPS/example.data b/...owExamples/QuickStart/LAMMPS/example.data → Examples/QuickStart/LAMMPS/example.data
diff --git a/...gbowExamples/QuickStart/LAMMPS/example.in → Examples/QuickStart/LAMMPS/example.in b/...gbowExamples/QuickStart/LAMMPS/example.in → Examples/QuickStart/LAMMPS/example.in
diff --git a/...ongbowExamples/QuickStart/NAMD/example.in → Examples/QuickStart/NAMD/example.in b/...ongbowExamples/QuickStart/NAMD/example.in → Examples/QuickStart/NAMD/example.in
diff --git a/.../QuickStart/NAMD/par_all27_prot_lipid.prm → .../QuickStart/NAMD/par_all27_prot_lipid.prm b/.../QuickStart/NAMD/par_all27_prot_lipid.prm → .../QuickStart/NAMD/par_all27_prot_lipid.prm
diff --git a/...ngbowExamples/QuickStart/NAMD/relres.coor → Examples/QuickStart/NAMD/relres.coor b/...ngbowExamples/QuickStart/NAMD/relres.coor → Examples/QuickStart/NAMD/relres.coor
diff --git a/...ongbowExamples/QuickStart/NAMD/relres.vel → Examples/QuickStart/NAMD/relres.vel b/...ongbowExamples/QuickStart/NAMD/relres.vel → Examples/QuickStart/NAMD/relres.vel
diff --git a/...ongbowExamples/QuickStart/NAMD/relres.xsc → Examples/QuickStart/NAMD/relres.xsc b/...ongbowExamples/QuickStart/NAMD/relres.xsc → Examples/QuickStart/NAMD/relres.xsc
diff --git a/...gbowExamples/QuickStart/NAMD/solvated.pdb → Examples/QuickStart/NAMD/solvated.pdb b/...gbowExamples/QuickStart/NAMD/solvated.pdb → Examples/QuickStart/NAMD/solvated.pdb
diff --git a/...gbowExamples/QuickStart/NAMD/solvated.psf → Examples/QuickStart/NAMD/solvated.psf b/...gbowExamples/QuickStart/NAMD/solvated.psf → Examples/QuickStart/NAMD/solvated.psf
diff --git a/Longbow/LongbowExamples/README → Examples/README b/Longbow/LongbowExamples/README → Examples/README
diff --git a/...les/ReplicateJob/par_all27_prot_lipid.prm → ...les/ReplicateJob/par_all27_prot_lipid.prm b/...les/ReplicateJob/par_all27_prot_lipid.prm → ...les/ReplicateJob/par_all27_prot_lipid.prm
diff --git a/...gbowExamples/ReplicateJob/rep1/example.in → Examples/ReplicateJob/rep1/example.in b/...gbowExamples/ReplicateJob/rep1/example.in → Examples/ReplicateJob/rep1/example.in
diff --git a/...bowExamples/ReplicateJob/rep1/relres.coor → Examples/ReplicateJob/rep1/relres.coor b/...bowExamples/ReplicateJob/rep1/relres.coor → Examples/ReplicateJob/rep1/relres.coor
diff --git a/...gbowExamples/ReplicateJob/rep1/relres.vel → Examples/ReplicateJob/rep1/relres.vel b/...gbowExamples/ReplicateJob/rep1/relres.vel → Examples/ReplicateJob/rep1/relres.vel
diff --git a/...gbowExamples/ReplicateJob/rep1/relres.xsc → Examples/ReplicateJob/rep1/relres.xsc b/...gbowExamples/ReplicateJob/rep1/relres.xsc → Examples/ReplicateJob/rep1/relres.xsc
diff --git a/...gbowExamples/ReplicateJob/rep2/example.in → Examples/ReplicateJob/rep2/example.in b/...gbowExamples/ReplicateJob/rep2/example.in → Examples/ReplicateJob/rep2/example.in
diff --git a/...bowExamples/ReplicateJob/rep2/relres.coor → Examples/ReplicateJob/rep2/relres.coor b/...bowExamples/ReplicateJob/rep2/relres.coor → Examples/ReplicateJob/rep2/relres.coor
diff --git a/...gbowExamples/ReplicateJob/rep2/relres.vel → Examples/ReplicateJob/rep2/relres.vel b/...gbowExamples/ReplicateJob/rep2/relres.vel → Examples/ReplicateJob/rep2/relres.vel
diff --git a/...gbowExamples/ReplicateJob/rep2/relres.xsc → Examples/ReplicateJob/rep2/relres.xsc b/...gbowExamples/ReplicateJob/rep2/relres.xsc → Examples/ReplicateJob/rep2/relres.xsc
diff --git a/...gbowExamples/ReplicateJob/rep3/example.in → Examples/ReplicateJob/rep3/example.in b/...gbowExamples/ReplicateJob/rep3/example.in → Examples/ReplicateJob/rep3/example.in
diff --git a/...bowExamples/ReplicateJob/rep3/relres.coor → Examples/ReplicateJob/rep3/relres.coor b/...bowExamples/ReplicateJob/rep3/relres.coor → Examples/ReplicateJob/rep3/relres.coor
diff --git a/...gbowExamples/ReplicateJob/rep3/relres.vel → Examples/ReplicateJob/rep3/relres.vel b/...gbowExamples/ReplicateJob/rep3/relres.vel → Examples/ReplicateJob/rep3/relres.vel
diff --git a/...gbowExamples/ReplicateJob/rep3/relres.xsc → Examples/ReplicateJob/rep3/relres.xsc b/...gbowExamples/ReplicateJob/rep3/relres.xsc → Examples/ReplicateJob/rep3/relres.xsc
diff --git a/...gbowExamples/ReplicateJob/rep4/example.in → Examples/ReplicateJob/rep4/example.in b/...gbowExamples/ReplicateJob/rep4/example.in → Examples/ReplicateJob/rep4/example.in
diff --git a/...bowExamples/ReplicateJob/rep4/relres.coor → Examples/ReplicateJob/rep4/relres.coor b/...bowExamples/ReplicateJob/rep4/relres.coor → Examples/ReplicateJob/rep4/relres.coor
diff --git a/...gbowExamples/ReplicateJob/rep4/relres.vel → Examples/ReplicateJob/rep4/relres.vel b/...gbowExamples/ReplicateJob/rep4/relres.vel → Examples/ReplicateJob/rep4/relres.vel
diff --git a/...gbowExamples/ReplicateJob/rep4/relres.xsc → Examples/ReplicateJob/rep4/relres.xsc b/...gbowExamples/ReplicateJob/rep4/relres.xsc → Examples/ReplicateJob/rep4/relres.xsc
diff --git a/...gbowExamples/ReplicateJob/rep5/example.in → Examples/ReplicateJob/rep5/example.in b/...gbowExamples/ReplicateJob/rep5/example.in → Examples/ReplicateJob/rep5/example.in
diff --git a/...bowExamples/ReplicateJob/rep5/relres.coor → Examples/ReplicateJob/rep5/relres.coor b/...bowExamples/ReplicateJob/rep5/relres.coor → Examples/ReplicateJob/rep5/relres.coor
diff --git a/...gbowExamples/ReplicateJob/rep5/relres.vel → Examples/ReplicateJob/rep5/relres.vel b/...gbowExamples/ReplicateJob/rep5/relres.vel → Examples/ReplicateJob/rep5/relres.vel
diff --git a/...gbowExamples/ReplicateJob/rep5/relres.xsc → Examples/ReplicateJob/rep5/relres.xsc b/...gbowExamples/ReplicateJob/rep5/relres.xsc → Examples/ReplicateJob/rep5/relres.xsc
diff --git a/...LongbowExamples/ReplicateJob/solvated.pdb → Examples/ReplicateJob/solvated.pdb b/...LongbowExamples/ReplicateJob/solvated.pdb → Examples/ReplicateJob/solvated.pdb
diff --git a/...LongbowExamples/ReplicateJob/solvated.psf → Examples/ReplicateJob/solvated.psf b/...LongbowExamples/ReplicateJob/solvated.psf → Examples/ReplicateJob/solvated.psf
diff --git a/Longbow/LongbowExamples/how-to-run → Examples/how-to-run b/Longbow/LongbowExamples/how-to-run → Examples/how-to-run