├── README.md ├── alchemical-free-energy ├── README.md ├── __init__.py ├── alchemical_analysis.py ├── amber │ ├── README.md │ ├── data │ │ ├── ti001 │ │ │ ├── ti001.en │ │ │ └── ti001.out.bz2 │ │ ├── ti002 │ │ │ ├── ti002.en │ │ │ └── ti002.out.bz2 │ │ ├── ti003 │ │ │ ├── ti003.en │ │ │ └── ti003.out.bz2 │ │ ├── ti004 │ │ │ ├── ti004.en │ │ │ └── ti004.out.bz2 │ │ └── ti005 │ │ │ ├── ti005.en │ │ │ └── ti005.out.bz2 │ ├── results.pickle │ ├── results.txt │ └── screen_printout.txt ├── gromacs │ ├── README.md │ ├── data │ │ ├── 3-methylindole-11steps-neighbors │ │ │ ├── dhdl.0.xvg │ │ │ ├── dhdl.1.xvg │ │ │ ├── dhdl.10.xvg │ │ │ ├── dhdl.2.xvg │ │ │ ├── dhdl.3.xvg │ │ │ ├── dhdl.4.xvg │ │ │ ├── dhdl.5.xvg │ │ │ ├── dhdl.6.xvg │ │ │ ├── dhdl.7.xvg │ │ │ ├── dhdl.8.xvg │ │ │ └── dhdl.9.xvg │ │ ├── 3-methylindole-11steps │ │ │ ├── dhdl.0.xvg │ │ │ ├── dhdl.1.xvg │ │ │ ├── dhdl.10.xvg │ │ │ ├── dhdl.2.xvg │ │ │ ├── dhdl.3.xvg │ │ │ ├── dhdl.4.xvg │ │ │ ├── dhdl.5.xvg │ │ │ ├── dhdl.6.xvg │ │ │ ├── dhdl.7.xvg │ │ │ ├── dhdl.8.xvg │ │ │ └── dhdl.9.xvg │ │ ├── 3-methylindole-38steps │ │ │ ├── dhdl.0.xvg │ │ │ ├── dhdl.1.xvg │ │ │ ├── dhdl.10.xvg │ │ │ ├── dhdl.11.xvg │ │ │ ├── dhdl.12.xvg │ │ │ ├── dhdl.13.xvg │ │ │ ├── dhdl.14.xvg │ │ │ ├── dhdl.15.xvg │ │ │ ├── dhdl.16.xvg │ │ │ ├── dhdl.17.xvg │ │ │ ├── dhdl.18.xvg │ │ │ ├── dhdl.19.xvg │ │ │ ├── dhdl.2.xvg │ │ │ ├── dhdl.20.xvg │ │ │ ├── dhdl.21.xvg │ │ │ ├── dhdl.22.xvg │ │ │ ├── dhdl.23.xvg │ │ │ ├── dhdl.24.xvg │ │ │ ├── dhdl.25.xvg │ │ │ ├── dhdl.26.xvg │ │ │ ├── dhdl.27.xvg │ │ │ ├── dhdl.28.xvg │ │ │ ├── dhdl.29.xvg │ │ │ ├── dhdl.3.xvg │ │ │ ├── dhdl.30.xvg │ │ │ ├── dhdl.31.xvg │ │ │ ├── dhdl.32.xvg │ │ │ ├── dhdl.33.xvg │ │ │ ├── dhdl.34.xvg │ │ │ ├── dhdl.35.xvg │ │ │ ├── dhdl.36.xvg │ │ │ ├── dhdl.37.xvg │ │ │ ├── dhdl.4.xvg │ │ │ ├── dhdl.5.xvg │ │ │ ├── dhdl.6.xvg │ │ │ ├── dhdl.7.xvg │ │ │ ├── dhdl.8.xvg │ │ │ └── dhdl.9.xvg │ │ └── convertdata.py │ ├── inputfiles │ │ └── 3-methylindole-38steps │ │ │ ├── trpo.gro │ │ │ ├── trpo.mdp │ │ │ └── trpo.top │ ├── output_11steps │ │ ├── O_MBAR.pdf │ │ ├── README.md │ │ ├── cfm.pdf │ │ ├── dF_state.pdf │ │ ├── dF_state_long.pdf │ │ ├── dhdl_TI.pdf │ │ ├── results.pickle │ │ ├── results.txt │ │ └── screen_printout.txt │ ├── output_11steps_neighbors │ │ ├── README.md │ │ ├── cfm.pdf │ │ ├── dF_state.pdf │ │ ├── dF_state_long.pdf │ │ ├── dhdl_TI.pdf │ │ ├── results.pickle │ │ ├── results.txt │ │ └── screen_printout.txt │ └── output_38steps │ │ ├── O_MBAR.pdf │ │ ├── README.md │ │ ├── cfm.pdf │ │ ├── dF_state.pdf │ │ ├── dF_state_long.pdf │ │ ├── dhdl_TI.pdf │ │ ├── results.pickle │ │ ├── results.txt │ │ └── screen_printout.txt ├── parsers │ ├── __init__.py │ ├── parser_amber.py │ ├── parser_gromacs.py │ ├── parser_sire.py │ └── unixlike.py └── sire │ ├── README.md │ ├── dF_state.pdf │ ├── dF_state_long.pdf │ ├── data │ ├── actual_grad_0000.dat │ ├── actual_grad_00954.dat │ ├── actual_grad_01464.dat │ ├── actual_grad_02061.dat │ ├── actual_grad_0244.dat │ ├── actual_grad_03454.dat │ ├── actual_grad_05000.dat │ ├── actual_grad_0544.dat │ ├── actual_grad_06545.dat │ ├── actual_grad_07269.dat │ ├── actual_grad_07938.dat │ ├── actual_grad_09045.dat │ ├── actual_grad_09455.dat │ ├── actual_grad_09755.dat │ ├── actual_grad_09938.dat │ └── actual_grad_1.dat │ ├── dhdl_TI.pdf │ ├── results.pickle │ ├── results.txt │ ├── screen_printout_1.txt │ ├── screen_printout_2.txt │ └── screen_printout_3.txt ├── constant-force-optical-trap ├── README ├── extract-data.py ├── force-bias-optical-trap.py ├── original-data │ └── 20R55_4T_data.xls.bz2 ├── output │ ├── counts-expected-0.out │ ├── counts-expected-1.out │ ├── counts-expected-10.out │ ├── counts-expected-11.out │ ├── counts-expected-12.out │ ├── counts-expected-13.out │ ├── counts-expected-14.out │ ├── counts-expected-15.out │ ├── counts-expected-2.out │ ├── counts-expected-3.out │ ├── counts-expected-4.out │ ├── counts-expected-5.out │ ├── counts-expected-6.out │ ├── counts-expected-7.out │ ├── counts-expected-8.out │ ├── counts-expected-9.out │ ├── counts-observed-0.out │ ├── counts-observed-1.out │ ├── counts-observed-10.out │ ├── counts-observed-11.out │ ├── counts-observed-12.out │ ├── counts-observed-13.out │ ├── counts-observed-14.out │ ├── counts-observed-15.out │ ├── counts-observed-2.out │ ├── counts-observed-3.out │ ├── counts-observed-4.out │ ├── counts-observed-5.out │ ├── counts-observed-6.out │ ├── counts-observed-7.out │ ├── counts-observed-8.out │ ├── counts-observed-9.out │ ├── pmf-expected-0.out │ ├── pmf-expected-1.out │ ├── pmf-expected-10.out │ ├── pmf-expected-11.out │ ├── pmf-expected-12.out │ ├── pmf-expected-13.out │ ├── pmf-expected-14.out │ ├── pmf-expected-15.out │ ├── pmf-expected-2.out │ ├── pmf-expected-3.out │ ├── pmf-expected-4.out │ ├── pmf-expected-5.out │ ├── pmf-expected-6.out │ ├── pmf-expected-7.out │ ├── pmf-expected-8.out │ ├── pmf-expected-9.out │ ├── pmf-observed-0.out │ ├── pmf-observed-1.out │ ├── pmf-observed-10.out │ ├── pmf-observed-11.out │ ├── pmf-observed-12.out │ ├── pmf-observed-13.out │ ├── pmf-observed-14.out │ ├── pmf-observed-15.out │ ├── pmf-observed-2.out │ ├── pmf-observed-3.out │ ├── pmf-observed-4.out │ ├── pmf-observed-5.out │ ├── pmf-observed-6.out │ ├── pmf-observed-7.out │ ├── pmf-observed-8.out │ ├── pmf-observed-9.out │ └── pmf-unbiased.out ├── plots │ ├── gnuplot.in │ ├── pmf-comparison-0.pdf │ ├── pmf-comparison-1.pdf │ ├── pmf-comparison-10.pdf │ ├── pmf-comparison-11.pdf │ ├── pmf-comparison-12.pdf │ ├── pmf-comparison-13.pdf │ ├── pmf-comparison-14.pdf │ ├── pmf-comparison-14.plot │ ├── pmf-comparison-15.pdf │ ├── pmf-comparison-2.pdf │ ├── pmf-comparison-3.pdf │ ├── pmf-comparison-4.pdf │ ├── pmf-comparison-5.pdf │ ├── pmf-comparison-6.pdf │ ├── pmf-comparison-7.pdf │ ├── pmf-comparison-8.pdf │ ├── pmf-comparison-9.pdf │ └── pmf-unbiased.pdf └── processed-data │ ├── 20R55_4T.forces │ └── 20R55_4T.trajectories ├── harmonic-oscillators ├── README.md ├── cumulative_probability_comparison_curves.pdf ├── harmonic-oscillators-distributions.py ├── harmonic-oscillators-distributions.sample_output ├── harmonic-oscillators.py ├── harmonic-oscillators.sample_output ├── oscillators.m └── oscillators.pdf ├── heat-capacity ├── README.md ├── energydata │ ├── TEMP0 │ │ ├── ener_box0.output │ │ └── simul0.output │ ├── TEMP1 │ │ ├── ener_box1.output │ │ └── simul1.output │ ├── TEMP10 │ │ ├── ener_box10.output │ │ └── simul10.output │ ├── TEMP11 │ │ ├── ener_box11.output │ │ └── simul11.output │ ├── TEMP12 │ │ ├── ener_box12.output │ │ └── simul12.output │ ├── TEMP13 │ │ ├── ener_box13.output │ │ └── simul13.output │ ├── TEMP14 │ │ ├── ener_box14.output │ │ └── simul14.output │ ├── TEMP15 │ │ ├── ener_box15.output │ │ └── simul15.output │ ├── TEMP2 │ │ ├── ener_box2.output │ │ └── simul2.output │ ├── TEMP3 │ │ ├── ener_box3.output │ │ └── simul3.output │ ├── TEMP4 │ │ ├── ener_box4.output │ │ └── simul4.output │ ├── TEMP5 │ │ ├── ener_box5.output │ │ └── simul5.output │ ├── TEMP6 │ │ ├── ener_box6.output │ │ └── simul6.output │ ├── TEMP7 │ │ ├── ener_box7.output │ │ └── simul7.output │ ├── TEMP8 │ │ ├── ener_box8.output │ │ └── simul8.output │ └── TEMP9 │ │ ├── ener_box9.output │ │ └── simul9.output ├── heat-capacity.py ├── heat-capacity.py.sample_out ├── heat-capacity.py.sample_out_bootstrap └── heat-capacity.py.sample_out_no_bootstrap ├── parallel-tempering-2dpmf ├── README.md ├── data │ ├── README.md │ ├── backbone-torsions │ │ ├── 0.phi │ │ ├── 0.psi │ │ ├── 1.phi │ │ ├── 1.psi │ │ ├── 10.phi │ │ ├── 10.psi │ │ ├── 11.phi │ │ ├── 11.psi │ │ ├── 12.phi │ │ ├── 12.psi │ │ ├── 13.phi │ │ ├── 13.psi │ │ ├── 14.phi │ │ ├── 14.psi │ │ ├── 15.phi │ │ ├── 15.psi │ │ ├── 16.phi │ │ ├── 16.psi │ │ ├── 17.phi │ │ ├── 17.psi │ │ ├── 18.phi │ │ ├── 18.psi │ │ ├── 19.phi │ │ ├── 19.psi │ │ ├── 2.phi │ │ ├── 2.psi │ │ ├── 20.phi │ │ ├── 20.psi │ │ ├── 21.phi │ │ ├── 21.psi │ │ ├── 22.phi │ │ ├── 22.psi │ │ ├── 23.phi │ │ ├── 23.psi │ │ ├── 24.phi │ │ ├── 24.psi │ │ ├── 25.phi │ │ ├── 25.psi │ │ ├── 26.phi │ │ ├── 26.psi │ │ ├── 27.phi │ │ ├── 27.psi │ │ ├── 28.phi │ │ ├── 28.psi │ │ ├── 29.phi │ │ ├── 29.psi │ │ ├── 3.phi │ │ ├── 3.psi │ │ ├── 30.phi │ │ ├── 30.psi │ │ ├── 31.phi │ │ ├── 31.psi │ │ ├── 32.phi │ │ ├── 32.psi │ │ ├── 33.phi │ │ ├── 33.psi │ │ ├── 34.phi │ │ ├── 34.psi │ │ ├── 35.phi │ │ ├── 35.psi │ │ ├── 36.phi │ │ ├── 36.psi │ │ ├── 37.phi │ │ ├── 37.psi │ │ ├── 38.phi │ │ ├── 38.psi │ │ ├── 39.phi │ │ ├── 39.psi │ │ ├── 4.phi │ │ ├── 4.psi │ │ ├── 5.phi │ │ ├── 5.psi │ │ ├── 6.phi │ │ ├── 6.psi │ │ ├── 7.phi │ │ ├── 7.psi │ │ ├── 8.phi │ │ ├── 8.psi │ │ ├── 9.phi │ │ └── 9.psi │ ├── configurations │ │ ├── a1e.equil_all.pdb │ │ └── a1e.solute-only.pdb │ ├── end-to-end-distance │ │ ├── 0.dist │ │ ├── 1.dist │ │ ├── 10.dist │ │ ├── 11.dist │ │ ├── 12.dist │ │ ├── 13.dist │ │ ├── 14.dist │ │ ├── 15.dist │ │ ├── 16.dist │ │ ├── 17.dist │ │ ├── 18.dist │ │ ├── 19.dist │ │ ├── 2.dist │ │ ├── 20.dist │ │ ├── 21.dist │ │ ├── 22.dist │ │ ├── 23.dist │ │ ├── 24.dist │ │ ├── 25.dist │ │ ├── 26.dist │ │ ├── 27.dist │ │ ├── 28.dist │ │ ├── 29.dist │ │ ├── 3.dist │ │ ├── 30.dist │ │ ├── 31.dist │ │ ├── 32.dist │ │ ├── 33.dist │ │ ├── 34.dist │ │ ├── 35.dist │ │ ├── 36.dist │ │ ├── 37.dist │ │ ├── 38.dist │ │ ├── 39.dist │ │ ├── 4.dist │ │ ├── 5.dist │ │ ├── 6.dist │ │ ├── 7.dist │ │ ├── 8.dist │ │ └── 9.dist │ ├── energies │ │ └── potential-energies │ ├── replica-indices │ └── temperatures ├── parallel-tempering-2dpmf.py └── parallel-tempering-2dpmf.sampleoutput └── umbrella-sampling-pmf ├── README ├── assumedatauncorrelated.output.txt ├── data ├── centers.dat ├── prod0_dihed.xvg ├── prod0_energies.xvg ├── prod10_dihed.xvg ├── prod10_energies.xvg ├── prod11_dihed.xvg ├── prod11_energies.xvg ├── prod12_dihed.xvg ├── prod12_energies.xvg ├── prod13_dihed.xvg ├── prod13_energies.xvg ├── prod14_dihed.xvg ├── prod14_energies.xvg ├── prod15_dihed.xvg ├── prod15_energies.xvg ├── prod16_dihed.xvg ├── prod16_energies.xvg ├── prod17_dihed.xvg ├── prod17_energies.xvg ├── prod18_dihed.xvg ├── prod18_energies.xvg ├── prod19_dihed.xvg ├── prod19_energies.xvg ├── prod1_dihed.xvg ├── prod1_energies.xvg ├── prod20_dihed.xvg ├── prod20_energies.xvg ├── prod21_dihed.xvg ├── prod21_energies.xvg ├── prod22_dihed.xvg ├── prod22_energies.xvg ├── prod23_dihed.xvg ├── prod23_energies.xvg ├── prod24_dihed.xvg ├── prod24_energies.xvg ├── prod25_dihed.xvg ├── prod25_energies.xvg ├── prod2_dihed.xvg ├── prod2_energies.xvg ├── prod3_dihed.xvg ├── prod3_energies.xvg ├── prod4_dihed.xvg ├── prod4_energies.xvg ├── prod5_dihed.xvg ├── prod5_energies.xvg ├── prod6_dihed.xvg ├── prod6_energies.xvg ├── prod7_dihed.xvg ├── prod7_energies.xvg ├── prod8_dihed.xvg ├── prod8_energies.xvg ├── prod9_dihed.xvg └── prod9_energies.xvg ├── pmf.out ├── pmf.pdf ├── umbrella-sampling.py ├── umbrella-sampling.sample_output └── wham ├── PMF_144 ├── PMF_18 ├── PMF_288 ├── PMF_36 ├── PMF_72 ├── centers.dat ├── data ├── 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