CODE_OF_CONDUCT.md
LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
versioneer.py
ensemble_md/__init__.py
ensemble_md/_version.py
ensemble_md/replica_exchange_EE.py
ensemble_md.egg-info/PKG-INFO
ensemble_md.egg-info/SOURCES.txt
ensemble_md.egg-info/dependency_links.txt
ensemble_md.egg-info/entry_points.txt
ensemble_md.egg-info/requires.txt
ensemble_md.egg-info/top_level.txt
ensemble_md/analysis/analyze_free_energy.py
ensemble_md/analysis/analyze_matrix.py
ensemble_md/analysis/analyze_traj.py
ensemble_md/analysis/clustering.py
ensemble_md/analysis/msm_analysis.py
ensemble_md/analysis/synthesize_data.py
ensemble_md/cli/analyze_REXEE.py
ensemble_md/cli/explore_REXEE.py
ensemble_md/cli/run_REXEE.py
ensemble_md/data/README.md
ensemble_md/data/instruction.md
ensemble_md/data/CB7-10/complex/complex.gro
ensemble_md/data/CB7-10/complex/complex.top
ensemble_md/data/CB7-10/complex/fixed_weight.mdp
ensemble_md/data/CB7-10/complex/params.yaml
ensemble_md/data/CB7-10/complex/weight_updating.mdp
ensemble_md/data/CB7-10/complex/itp_files/10_GMX.itp
ensemble_md/data/CB7-10/complex/itp_files/10atomtypes.itp
ensemble_md/data/CB7-10/complex/itp_files/cucurbit_7_uril_GMX.itp
ensemble_md/data/CB7-10/solvent/fixed_weight.mdp
ensemble_md/data/CB7-10/solvent/ligand.gro
ensemble_md/data/CB7-10/solvent/ligand.top
ensemble_md/data/CB7-10/solvent/weight_updating.mdp
ensemble_md/data/anthracene/HREX.mdp
ensemble_md/data/anthracene/anthracene.gro
ensemble_md/data/anthracene/anthracene.top
ensemble_md/data/anthracene/fixed_weight.mdp
ensemble_md/data/anthracene/params.yaml
ensemble_md/data/anthracene/weight_updating.mdp
ensemble_md/tests/__init__.py
ensemble_md/tests/test_analyze_free_energy.py
ensemble_md/tests/test_analyze_matrix.py
ensemble_md/tests/test_analyze_traj.py
ensemble_md/tests/test_clustering.py
ensemble_md/tests/test_gmx_parser.py
ensemble_md/tests/test_mpi_func.py
ensemble_md/tests/test_replica_exchange_EE.py
ensemble_md/tests/test_synthesize_data.py
ensemble_md/tests/test_utils.py
ensemble_md/tests/data/cluster.log
ensemble_md/tests/data/expanded.mdp
ensemble_md/tests/data/expanded_pull.mdp
ensemble_md/tests/data/pullx.xvg
ensemble_md/tests/data/run_REXEE_log.txt
ensemble_md/tests/data/sys.gro
ensemble_md/tests/data/sys.ndx
ensemble_md/tests/data/sys.top
ensemble_md/tests/data/traj.xvg
ensemble_md/tests/data/dhdl/dhdl_0.xvg
ensemble_md/tests/data/dhdl/dhdl_1.xvg
ensemble_md/tests/data/dhdl/dhdl_2.xvg
ensemble_md/tests/data/dhdl/dhdl_3.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_0/iteration_0/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_0/iteration_1/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_0/iteration_2/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_1/iteration_0/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_1/iteration_1/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_1/iteration_2/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_2/iteration_0/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_2/iteration_1/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_2/iteration_2/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_3/iteration_0/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_3/iteration_1/dhdl.xvg
ensemble_md/tests/data/dhdl/simulation_example/sim_3/iteration_2/dhdl.xvg
ensemble_md/tests/data/log/EXE.log
ensemble_md/tests/data/log/EXE_0.log
ensemble_md/tests/data/log/EXE_1.log
ensemble_md/tests/data/log/EXE_2.log
ensemble_md/tests/data/log/EXE_3.log
ensemble_md/tests/data/log/HREX.log
ensemble_md/tests/data/log/case2_1.log
ensemble_md/tests/data/log/case2_2.log
ensemble_md/tests/data/log/case3.log
ensemble_md/tests/data/mdp/compare_1.mdp
ensemble_md/tests/data/mdp/compare_2.mdp
ensemble_md/tests/data/mdp/compare_3.mdp
ensemble_md/utils/exceptions.py
ensemble_md/utils/gmx_parser.py
ensemble_md/utils/utils.py