Reading data/3-methylindole-38steps//dhdl.0.xvg... Reading data/3-methylindole-38steps//dhdl.1.xvg... Reading data/3-methylindole-38steps//dhdl.2.xvg... Reading data/3-methylindole-38steps//dhdl.3.xvg... Reading data/3-methylindole-38steps//dhdl.4.xvg... Reading data/3-methylindole-38steps//dhdl.5.xvg... Reading data/3-methylindole-38steps//dhdl.6.xvg... Reading data/3-methylindole-38steps//dhdl.7.xvg... Reading data/3-methylindole-38steps//dhdl.8.xvg... Reading data/3-methylindole-38steps//dhdl.9.xvg... Reading data/3-methylindole-38steps//dhdl.10.xvg... Reading data/3-methylindole-38steps//dhdl.11.xvg... Reading data/3-methylindole-38steps//dhdl.12.xvg... Reading data/3-methylindole-38steps//dhdl.13.xvg... Reading data/3-methylindole-38steps//dhdl.14.xvg... Reading data/3-methylindole-38steps//dhdl.15.xvg... Reading data/3-methylindole-38steps//dhdl.16.xvg... Reading data/3-methylindole-38steps//dhdl.17.xvg... Reading data/3-methylindole-38steps//dhdl.18.xvg... Reading data/3-methylindole-38steps//dhdl.19.xvg... Reading data/3-methylindole-38steps//dhdl.20.xvg... Reading data/3-methylindole-38steps//dhdl.21.xvg... Reading data/3-methylindole-38steps//dhdl.22.xvg... Reading data/3-methylindole-38steps//dhdl.23.xvg... Reading data/3-methylindole-38steps//dhdl.24.xvg... Reading data/3-methylindole-38steps//dhdl.25.xvg... Reading data/3-methylindole-38steps//dhdl.26.xvg... Reading data/3-methylindole-38steps//dhdl.27.xvg... Reading data/3-methylindole-38steps//dhdl.28.xvg... Reading data/3-methylindole-38steps//dhdl.29.xvg... Reading data/3-methylindole-38steps//dhdl.30.xvg... Reading data/3-methylindole-38steps//dhdl.31.xvg... Reading data/3-methylindole-38steps//dhdl.32.xvg... Reading data/3-methylindole-38steps//dhdl.33.xvg... Reading data/3-methylindole-38steps//dhdl.34.xvg... Reading data/3-methylindole-38steps//dhdl.35.xvg... Reading data/3-methylindole-38steps//dhdl.36.xvg... Reading data/3-methylindole-38steps//dhdl.37.xvg... Correlation times: [ 1.65143127 2.17037854 1.22004013 1.01560048 1.7056375 5.16063757 1.1118296 1.73381596 2.38261244 3.40357847 2.85206571 1. 1. 1.44615472 1.35065093 1.2494565 1.13634513 1.06461452 1.58433517 1.08573441 1.43722146 1.09011557 1.60403516 1.40720421 1.34337365 1. 1.22053131 1. 1.21429908 1. 1.25879852 1.05412477 1.16544342 1.13188841 1.305765 1. 1.10858668 1. ] number of uncorrelated samples: [243 185 329 395 235 78 361 231 169 118 141 401 401 277 297 321 353 377 253 369 279 368 250 285 299 401 329 401 330 401 319 380 344 354 307 401 362 401] Solving for MBAR estimate... Using embedded C++ helper code. K = 38, L = 38, N_max = 401, total samples = 11745 N_k = [243 185 329 395 235 78 361 231 169 118 141 401 401 277 297 321 353 377 253 369 279 368 250 285 299 401 329 401 330 401 319 380 344 354 307 401 362 401] Initializing free energies to zero. relative_change = 1.000 iteration 0 : DeltaF = 2.802 relative_change = 0.000 iteration 1 : DeltaF = 2.802 relative_change = 0.000 Convergence achieved. Converged to tolerance of 5.918509e-09 in 2 iterations (5 function evaluations) DeltaF = 2.802 relative_change = 1.000 iteration 0 : DeltaF = 2.455 relative_change = 0.000 iteration 1 : DeltaF = 2.454 relative_change = 0.000 Convergence achieved. Converged to tolerance of 2.893831e-08 in 2 iterations (5 function evaluations) DeltaF = 2.454 relative_change = 1.000 iteration 0 : DeltaF = 2.153 relative_change = 0.000 iteration 1 : DeltaF = 2.153 relative_change = 0.000 Convergence achieved. Converged to tolerance of 2.345749e-09 in 2 iterations (5 function evaluations) DeltaF = 2.153 relative_change = 1.000 iteration 0 : DeltaF = 1.865 relative_change = 0.000 iteration 1 : DeltaF = 1.865 relative_change = 0.000 Convergence achieved. Converged to tolerance of 4.415575e-09 in 2 iterations (5 function evaluations) DeltaF = 1.865 relative_change = 1.000 iteration 0 : DeltaF = 1.592 relative_change = 0.000 iteration 1 : DeltaF = 1.592 relative_change = 0.000 Convergence achieved. Converged to tolerance of 2.221350e-09 in 2 iterations (5 function evaluations) DeltaF = 1.592 relative_change = 1.000 iteration 0 : DeltaF = 1.369 relative_change = 0.000 iteration 1 : DeltaF = 1.369 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.388997e-08 in 2 iterations (5 function evaluations) DeltaF = 1.369 relative_change = 1.000 iteration 0 : DeltaF = 1.147 relative_change = 0.000 iteration 1 : DeltaF = 1.147 relative_change = 0.000 Convergence achieved. Converged to tolerance of 6.224223e-10 in 2 iterations (5 function evaluations) DeltaF = 1.147 relative_change = 1.000 iteration 0 : DeltaF = 0.955 relative_change = 0.000 iteration 1 : DeltaF = 0.955 relative_change = 0.000 Convergence achieved. Converged to tolerance of 4.358926e-09 in 2 iterations (5 function evaluations) DeltaF = 0.955 relative_change = 1.000 iteration 0 : DeltaF = 0.798 relative_change = 0.000 iteration 1 : DeltaF = 0.798 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.061883e-09 in 2 iterations (5 function evaluations) DeltaF = 0.798 relative_change = 1.000 iteration 0 : DeltaF = 0.625 relative_change = 0.000 iteration 1 : DeltaF = 0.625 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.576768e-09 in 2 iterations (5 function evaluations) DeltaF = 0.625 relative_change = 1.000 iteration 0 : DeltaF = -2.028 relative_change = 0.000 iteration 1 : DeltaF = -2.027 relative_change = 0.000 Convergence achieved. Converged to tolerance of 2.042801e-07 in 2 iterations (5 function evaluations) DeltaF = -2.027 relative_change = 1.000 iteration 0 : DeltaF = -0.419 relative_change = 0.001 iteration 1 : DeltaF = -0.420 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.957260e-06 in 2 iterations (5 function evaluations) DeltaF = -0.420 relative_change = 1.000 iteration 0 : DeltaF = 0.322 relative_change = 0.001 iteration 1 : DeltaF = 0.322 relative_change = 0.000 Convergence achieved. Converged to tolerance of 3.958865e-07 in 2 iterations (5 function evaluations) DeltaF = 0.322 relative_change = 1.000 iteration 0 : DeltaF = 0.296 relative_change = 0.000 iteration 1 : DeltaF = 0.296 relative_change = 0.000 Convergence achieved. Converged to tolerance of 6.575569e-10 in 2 iterations (5 function evaluations) DeltaF = 0.296 relative_change = 1.000 iteration 0 : DeltaF = 0.343 relative_change = 0.000 iteration 1 : DeltaF = 0.343 relative_change = 0.000 Convergence achieved. Converged to tolerance of 6.177759e-09 in 2 iterations (5 function evaluations) DeltaF = 0.343 relative_change = 1.000 iteration 0 : DeltaF = 0.366 relative_change = 0.000 iteration 1 : DeltaF = 0.366 relative_change = 0.000 Convergence achieved. Converged to tolerance of 8.784943e-09 in 2 iterations (5 function evaluations) DeltaF = 0.366 relative_change = 1.000 iteration 0 : DeltaF = 0.342 relative_change = 0.000 iteration 1 : DeltaF = 0.342 relative_change = 0.000 Convergence achieved. Converged to tolerance of 8.526035e-10 in 2 iterations (5 function evaluations) DeltaF = 0.342 relative_change = 1.000 iteration 0 : DeltaF = 0.290 relative_change = 0.000 iteration 1 : DeltaF = 0.290 relative_change = 0.000 Convergence achieved. Converged to tolerance of 3.264757e-08 in 2 iterations (5 function evaluations) DeltaF = 0.290 relative_change = 1.000 iteration 0 : DeltaF = 0.095 relative_change = 0.000 iteration 1 : DeltaF = 0.095 relative_change = 0.000 Convergence achieved. Converged to tolerance of 7.124692e-08 in 2 iterations (5 function evaluations) DeltaF = 0.095 relative_change = 1.000 iteration 0 : DeltaF = 0.026 relative_change = 0.000 iteration 1 : DeltaF = 0.026 relative_change = 0.000 Convergence achieved. Converged to tolerance of 8.437214e-10 in 2 iterations (5 function evaluations) DeltaF = 0.026 relative_change = 1.000 iteration 0 : DeltaF = -0.023 relative_change = 0.001 iteration 1 : DeltaF = -0.023 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.799104e-07 in 2 iterations (5 function evaluations) DeltaF = -0.023 relative_change = 1.000 iteration 0 : DeltaF = -0.074 relative_change = 0.000 iteration 1 : DeltaF = -0.074 relative_change = 0.000 Convergence achieved. Converged to tolerance of 8.874199e-10 in 2 iterations (5 function evaluations) DeltaF = -0.074 relative_change = 1.000 iteration 0 : DeltaF = -0.102 relative_change = 0.000 iteration 1 : DeltaF = -0.102 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.192055e-09 in 2 iterations (5 function evaluations) DeltaF = -0.102 relative_change = 1.000 iteration 0 : DeltaF = -0.197 relative_change = 0.000 iteration 1 : DeltaF = -0.197 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.615182e-10 in 2 iterations (5 function evaluations) DeltaF = -0.197 relative_change = 1.000 iteration 0 : DeltaF = -0.277 relative_change = 0.000 iteration 1 : DeltaF = -0.277 relative_change = 0.000 Convergence achieved. Converged to tolerance of 6.182733e-09 in 2 iterations (5 function evaluations) DeltaF = -0.277 relative_change = 1.000 iteration 0 : DeltaF = -0.384 relative_change = 0.000 iteration 1 : DeltaF = -0.384 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.807021e-09 in 2 iterations (5 function evaluations) DeltaF = -0.384 relative_change = 1.000 iteration 0 : DeltaF = -0.512 relative_change = 0.000 iteration 1 : DeltaF = -0.512 relative_change = 0.000 Convergence achieved. Converged to tolerance of 3.003856e-10 in 2 iterations (5 function evaluations) DeltaF = -0.512 relative_change = 1.000 iteration 0 : DeltaF = -0.626 relative_change = 0.000 iteration 1 : DeltaF = -0.626 relative_change = 0.000 Convergence achieved. Converged to tolerance of 9.640804e-09 in 2 iterations (5 function evaluations) DeltaF = -0.626 relative_change = 1.000 iteration 0 : DeltaF = -0.713 relative_change = 0.000 iteration 1 : DeltaF = -0.713 relative_change = 0.000 Convergence achieved. Converged to tolerance of 5.831711e-09 in 2 iterations (5 function evaluations) DeltaF = -0.713 relative_change = 1.000 iteration 0 : DeltaF = -0.771 relative_change = 0.000 iteration 1 : DeltaF = -0.771 relative_change = 0.000 Convergence achieved. Converged to tolerance of 6.653343e-09 in 2 iterations (5 function evaluations) DeltaF = -0.771 relative_change = 1.000 iteration 0 : DeltaF = -0.772 relative_change = 0.000 iteration 1 : DeltaF = -0.772 relative_change = 0.000 Convergence achieved. Converged to tolerance of 5.444509e-11 in 2 iterations (5 function evaluations) DeltaF = -0.772 relative_change = 1.000 iteration 0 : DeltaF = -0.709 relative_change = 0.000 iteration 1 : DeltaF = -0.709 relative_change = 0.000 Convergence achieved. Converged to tolerance of 8.056130e-11 in 2 iterations (5 function evaluations) DeltaF = -0.709 relative_change = 1.000 iteration 0 : DeltaF = -0.616 relative_change = 0.000 iteration 1 : DeltaF = -0.616 relative_change = 0.000 Convergence achieved. Converged to tolerance of 9.551076e-15 in 2 iterations (5 function evaluations) DeltaF = -0.616 relative_change = 1.000 iteration 0 : DeltaF = -0.523 relative_change = 0.000 iteration 1 : DeltaF = -0.523 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.198339e-11 in 2 iterations (5 function evaluations) DeltaF = -0.523 relative_change = 1.000 iteration 0 : DeltaF = -0.787 relative_change = 0.000 iteration 1 : DeltaF = -0.787 Convergence achieved. Converged to tolerance of -5.000000e+00 in 2 iterations (5 function evaluations) DeltaF = -0.787 relative_change = 1.000 iteration 0 : DeltaF = -0.422 relative_change = 0.000 iteration 1 : DeltaF = -0.422 relative_change = 0.000 Convergence achieved. Converged to tolerance of 3.863316e-11 in 2 iterations (5 function evaluations) DeltaF = -0.422 relative_change = 1.000 iteration 0 : DeltaF = -0.072 relative_change = 0.000 iteration 1 : DeltaF = -0.072 relative_change = 0.000 Convergence achieved. Converged to tolerance of 1.152843e-12 in 2 iterations (5 function evaluations) DeltaF = -0.072 initialized MBAR with BAR with values: f_k = [ 0. 2.80198977 5.25643618 7.40906931 9.27383803 10.86572746 12.23461839 13.3820071 14.33667607 15.13443568 15.75927632 13.73196054 13.31228073 13.63410099 13.93026216 14.27300366 14.63887022 14.9805671 15.27026515 15.36552763 15.39139675 15.36870556 15.29459371 15.19270103 14.99570732 14.71908072 14.33477808 13.82291564 13.19699241 12.48429633 11.71284752 10.94117401 10.23202773 9.6159524 9.09304458 8.30569382 7.88397431 7.8121563 ] Determining dimensionless free energies by Newton-Raphson iteration. There are 38 states with samples. Newton-Raphson iteration 0 current f_k for states with samples = 0.0000 2.8033 5.2587 7.4098 9.2722 10.8627 12.2295 13.3766 14.3322 15.1296 15.7552 13.7267 13.3062 13.6310 13.9300 14.2756 14.6429 14.9853 15.2731 15.3689 15.3952 15.3739 15.3014 15.1977 15.0007 14.7227 14.3369 13.8248 13.1989 12.4864 11.7167 10.9473 10.2386 9.6207 9.0956 8.3068 7.8857 7.8151 relative max_delta = 4.325497e-04 Newton-Raphson iteration 1 current f_k for states with samples = 0.0000 2.8156 5.2795 7.4166 9.2574 10.8353 12.1831 13.3284 14.2917 15.0864 15.7186 13.6793 13.2513 13.6035 13.9277 14.2991 14.6793 15.0277 15.2987 15.3992 15.4290 15.4202 15.3626 15.2425 15.0455 14.7547 14.3561 13.8413 13.2160 12.5053 11.7515 11.0023 10.2972 9.6635 9.1181 8.3169 7.9010 7.8418 relative max_delta = 3.892121e-03 Newton-Raphson iteration 2 current f_k for states with samples = 0.0000 2.8156 5.2793 7.4166 9.2575 10.8354 12.1831 13.3284 14.2918 15.0865 15.7186 13.6794 13.2510 13.6033 13.9275 14.2988 14.6788 15.0272 15.2983 15.3988 15.4287 15.4198 15.3619 15.2421 15.0450 14.7544 14.3556 13.8409 13.2156 12.5048 11.7511 11.0016 10.2964 9.6630 9.1177 8.3164 7.9005 7.8415 relative max_delta = 4.919866e-05 Newton-Raphson iteration 3 current f_k for states with samples = 0.0000 2.8156 5.2793 7.4166 9.2575 10.8354 12.1831 13.3284 14.2918 15.0865 15.7186 13.6794 13.2510 13.6033 13.9275 14.2988 14.6788 15.0272 15.2983 15.3988 15.4287 15.4198 15.3619 15.2421 15.0450 14.7544 14.3556 13.8409 13.2156 12.5048 11.7511 11.0016 10.2964 9.6630 9.1177 8.3164 7.9005 7.8415 relative max_delta = 3.042247e-09 Newton-Raphson iteration 4 current f_k for states with samples = 0.0000 2.8156 5.2793 7.4166 9.2575 10.8354 12.1831 13.3284 14.2918 15.0865 15.7186 13.6794 13.2510 13.6033 13.9275 14.2988 14.6788 15.0272 15.2983 15.3988 15.4287 15.4198 15.3619 15.2421 15.0450 14.7544 14.3556 13.8409 13.2156 12.5048 11.7511 11.0016 10.2964 9.6630 9.1177 8.3164 7.9005 7.8415 relative max_delta = 3.360904e-13 Converged to tolerance of 3.360904e-13 in 5 Newton-Raphson iterations. Recomputing all free energies... current f_k for all states = 0.0000 2.8156 5.2793 7.4166 9.2575 10.8354 12.1831 13.3284 14.2918 15.0865 15.7186 13.6794 13.2510 13.6033 13.9275 14.2988 14.6788 15.0272 15.2983 15.3988 15.4287 15.4198 15.3619 15.2421 15.0450 14.7544 14.3556 13.8409 13.2156 12.5048 11.7511 11.0016 10.2964 9.6630 9.1177 8.3164 7.9005 7.8415 Final dimensionless free energies f_k = [ 0. 2.81555765 5.27931637 7.41656205 9.25745877 10.83540025 12.18307125 13.32839017 14.29182819 15.08646442 15.71864188 13.67936772 13.25102428 13.60325627 13.92750441 14.29880567 14.67881122 15.02720165 15.29831519 15.39882341 15.42866477 15.41979478 15.36193236 15.24212373 15.04504045 14.75436925 14.35563818 13.84087891 13.21557508 12.50484742 11.75107679 11.00161247 10.29641525 9.66304519 9.11765092 8.3163781 7.90052945 7.84146241] Computing normalized weights... Estimating entropic and enthalpic contributions... Free energy difference (dG) between states 0 and 37 7.841 +/- 0.151 kT 19.434 +/- 0.375 kJ*mol^-1 Enthalpic contribution (dH) by endpoint method 55.477 +/- 4.934 kT 137.491 +/- 12.227 kJ*mol^-1 Entropic contribution (T*dS) by endpoint method 47.636 +/- 4.936 kT 396.165 +/- 41.050 J*mol^-1*K^-1 Enthalpic contribution (dH) by MBAR 47.368 +/- 4.036 kT 117.393 +/- 10.002 kJ*mol^-1 Entropic contribution (T*dS) by MBAR 39.526 +/- 4.039 kT Entropy (dS) by MBAR 328.723 +/- 33.594 J*mol^-1*K^-1 Note that the enthalpic and entropic contributions have correlated errors, since dG = dH - T*dS.