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add umbrella sampling tutorial (#24)
* add umbrella sampling tutorial * Improve explanation, theory, references, and figures * fix typos * code formatting and text fixes * links in markdown * minor changes * minor changes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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| TITLE DECA-ALA | ||
| ATOM 1 1HH3 ACE 1 6.138 4.146 -3.223 1.00 0.00 | ||
| ATOM 2 CH3 ACE 1 6.844 3.333 -3.064 1.00 0.00 | ||
| ATOM 3 2HH3 ACE 1 7.542 3.605 -2.273 1.00 0.00 | ||
| ATOM 4 3HH3 ACE 1 7.394 3.142 -3.984 1.00 0.00 | ||
| ATOM 5 C ACE 1 6.095 2.085 -2.664 1.00 0.00 | ||
| ATOM 6 O ACE 1 4.870 2.104 -2.562 1.00 0.00 | ||
| ATOM 7 N ALA 2 6.826 0.999 -2.415 1.00 0.00 | ||
| ATOM 8 H ALA 2 7.827 1.065 -2.529 1.00 0.00 | ||
| ATOM 9 CA ALA 2 6.255 -0.311 -2.082 1.00 0.00 | ||
| ATOM 10 HA ALA 2 5.611 -0.625 -2.905 1.00 0.00 | ||
| ATOM 11 CB ALA 2 7.405 -1.320 -1.966 1.00 0.00 | ||
| ATOM 12 HB1 ALA 2 8.078 -1.036 -1.155 1.00 0.00 | ||
| ATOM 13 HB2 ALA 2 7.001 -2.312 -1.760 1.00 0.00 | ||
| ATOM 14 HB3 ALA 2 7.964 -1.357 -2.902 1.00 0.00 | ||
| ATOM 15 C ALA 2 5.391 -0.293 -0.803 1.00 0.00 | ||
| ATOM 16 O ALA 2 4.342 -0.937 -0.761 1.00 0.00 | ||
| ATOM 17 N ALA 3 5.779 0.486 0.214 1.00 0.00 | ||
| ATOM 18 H ALA 3 6.661 0.970 0.133 1.00 0.00 | ||
| ATOM 19 CA ALA 3 4.999 0.663 1.443 1.00 0.00 | ||
| ATOM 20 HA ALA 3 4.769 -0.321 1.857 1.00 0.00 | ||
| ATOM 21 CB ALA 3 5.863 1.418 2.462 1.00 0.00 | ||
| ATOM 22 HB1 ALA 3 6.121 2.408 2.082 1.00 0.00 | ||
| ATOM 23 HB2 ALA 3 5.312 1.529 3.396 1.00 0.00 | ||
| ATOM 24 HB3 ALA 3 6.778 0.857 2.660 1.00 0.00 | ||
| ATOM 25 C ALA 3 3.657 1.385 1.193 1.00 0.00 | ||
| ATOM 26 O ALA 3 2.625 0.977 1.730 1.00 0.00 | ||
| ATOM 27 N ALA 4 3.645 2.413 0.336 1.00 0.00 | ||
| ATOM 28 H ALA 4 4.515 2.694 -0.091 1.00 0.00 | ||
| ATOM 29 CA ALA 4 2.424 3.116 -0.068 1.00 0.00 | ||
| ATOM 30 HA ALA 4 1.867 3.391 0.829 1.00 0.00 | ||
| ATOM 31 CB ALA 4 2.815 4.408 -0.797 1.00 0.00 | ||
| ATOM 32 HB1 ALA 4 3.367 4.180 -1.709 1.00 0.00 | ||
| ATOM 33 HB2 ALA 4 1.913 4.964 -1.060 1.00 0.00 | ||
| ATOM 34 HB3 ALA 4 3.432 5.030 -0.147 1.00 0.00 | ||
| ATOM 35 C ALA 4 1.505 2.227 -0.929 1.00 0.00 | ||
| ATOM 36 O ALA 4 0.290 2.220 -0.726 1.00 0.00 | ||
| ATOM 37 N ALA 5 2.073 1.420 -1.834 1.00 0.00 | ||
| ATOM 38 H ALA 5 3.070 1.509 -1.999 1.00 0.00 | ||
| ATOM 39 CA ALA 5 1.328 0.431 -2.617 1.00 0.00 | ||
| ATOM 40 HA ALA 5 0.514 0.940 -3.136 1.00 0.00 | ||
| ATOM 41 CB ALA 5 2.268 -0.162 -3.674 1.00 0.00 | ||
| ATOM 42 HB1 ALA 5 3.094 -0.689 -3.195 1.00 0.00 | ||
| ATOM 43 HB2 ALA 5 1.716 -0.864 -4.301 1.00 0.00 | ||
| ATOM 44 HB3 ALA 5 2.667 0.633 -4.305 1.00 0.00 | ||
| ATOM 45 C ALA 5 0.699 -0.663 -1.728 1.00 0.00 | ||
| ATOM 46 O ALA 5 -0.472 -1.005 -1.906 1.00 0.00 | ||
| ATOM 47 N ALA 6 1.434 -1.164 -0.728 1.00 0.00 | ||
| ATOM 48 H ALA 6 2.409 -0.894 -0.661 1.00 0.00 | ||
| ATOM 49 CA ALA 6 0.921 -2.119 0.258 1.00 0.00 | ||
| ATOM 50 HA ALA 6 0.503 -2.976 -0.273 1.00 0.00 | ||
| ATOM 51 CB ALA 6 2.093 -2.615 1.114 1.00 0.00 | ||
| ATOM 52 HB1 ALA 6 2.546 -1.785 1.656 1.00 0.00 | ||
| ATOM 53 HB2 ALA 6 1.733 -3.354 1.832 1.00 0.00 | ||
| ATOM 54 HB3 ALA 6 2.845 -3.082 0.478 1.00 0.00 | ||
| ATOM 55 C ALA 6 -0.204 -1.519 1.125 1.00 0.00 | ||
| ATOM 56 O ALA 6 -1.225 -2.173 1.343 1.00 0.00 | ||
| ATOM 57 N ALA 7 -0.069 -0.260 1.562 1.00 0.00 | ||
| ATOM 58 H ALA 7 0.813 0.216 1.405 1.00 0.00 | ||
| ATOM 59 CA ALA 7 -1.119 0.457 2.290 1.00 0.00 | ||
| ATOM 60 HA ALA 7 -1.408 -0.138 3.158 1.00 0.00 | ||
| ATOM 61 CB ALA 7 -0.542 1.785 2.798 1.00 0.00 | ||
| ATOM 62 HB1 ALA 7 -0.238 2.413 1.959 1.00 0.00 | ||
| ATOM 63 HB2 ALA 7 -1.299 2.313 3.380 1.00 0.00 | ||
| ATOM 64 HB3 ALA 7 0.322 1.595 3.436 1.00 0.00 | ||
| ATOM 65 C ALA 7 -2.385 0.673 1.434 1.00 0.00 | ||
| ATOM 66 O ALA 7 -3.498 0.442 1.911 1.00 0.00 | ||
| ATOM 67 N ALA 8 -2.230 1.043 0.157 1.00 0.00 | ||
| ATOM 68 H ALA 8 -1.296 1.266 -0.171 1.00 0.00 | ||
| ATOM 69 CA ALA 8 -3.340 1.187 -0.789 1.00 0.00 | ||
| ATOM 70 HA ALA 8 -4.075 1.870 -0.359 1.00 0.00 | ||
| ATOM 71 CB ALA 8 -2.799 1.819 -2.078 1.00 0.00 | ||
| ATOM 72 HB1 ALA 8 -2.056 1.166 -2.537 1.00 0.00 | ||
| ATOM 73 HB2 ALA 8 -3.619 1.973 -2.781 1.00 0.00 | ||
| ATOM 74 HB3 ALA 8 -2.342 2.784 -1.855 1.00 0.00 | ||
| ATOM 75 C ALA 8 -4.057 -0.150 -1.069 1.00 0.00 | ||
| ATOM 76 O ALA 8 -5.287 -0.181 -1.152 1.00 0.00 | ||
| ATOM 77 N ALA 9 -3.315 -1.261 -1.156 1.00 0.00 | ||
| ATOM 78 H ALA 9 -2.305 -1.167 -1.154 1.00 0.00 | ||
| ATOM 79 CA ALA 9 -3.880 -2.606 -1.280 1.00 0.00 | ||
| ATOM 80 HA ALA 9 -4.598 -2.610 -2.102 1.00 0.00 | ||
| ATOM 81 CB ALA 9 -2.748 -3.580 -1.635 1.00 0.00 | ||
| ATOM 82 HB1 ALA 9 -2.006 -3.608 -0.837 1.00 0.00 | ||
| ATOM 83 HB2 ALA 9 -3.158 -4.581 -1.774 1.00 0.00 | ||
| ATOM 84 HB3 ALA 9 -2.267 -3.265 -2.562 1.00 0.00 | ||
| ATOM 85 C ALA 9 -4.633 -3.046 -0.006 1.00 0.00 | ||
| ATOM 86 O ALA 9 -5.740 -3.582 -0.098 1.00 0.00 | ||
| ATOM 87 N ALA 10 -4.078 -2.775 1.182 1.00 0.00 | ||
| ATOM 88 H ALA 10 -3.146 -2.376 1.198 1.00 0.00 | ||
| ATOM 89 CA ALA 10 -4.714 -3.071 2.471 1.00 0.00 | ||
| ATOM 90 HA ALA 10 -4.996 -4.125 2.486 1.00 0.00 | ||
| ATOM 91 CB ALA 10 -3.681 -2.837 3.580 1.00 0.00 | ||
| ATOM 92 HB1 ALA 10 -3.374 -1.791 3.596 1.00 0.00 | ||
| ATOM 93 HB2 ALA 10 -4.117 -3.094 4.546 1.00 0.00 | ||
| ATOM 94 HB3 ALA 10 -2.806 -3.467 3.412 1.00 0.00 | ||
| ATOM 95 C ALA 10 -5.996 -2.247 2.716 1.00 0.00 | ||
| ATOM 96 O ALA 10 -6.949 -2.749 3.317 1.00 0.00 | ||
| ATOM 97 N ALA 11 -6.049 -1.006 2.218 1.00 0.00 | ||
| ATOM 98 H ALA 11 -5.204 -0.623 1.810 1.00 0.00 | ||
| ATOM 99 CA ALA 11 -7.237 -0.146 2.244 1.00 0.00 | ||
| ATOM 100 HA ALA 11 -7.666 -0.182 3.247 1.00 0.00 | ||
| ATOM 101 CB ALA 11 -6.777 1.294 1.978 1.00 0.00 | ||
| ATOM 102 HB1 ALA 11 -6.348 1.371 0.978 1.00 0.00 | ||
| ATOM 103 HB2 ALA 11 -7.628 1.972 2.053 1.00 0.00 | ||
| ATOM 104 HB3 ALA 11 -6.029 1.588 2.715 1.00 0.00 | ||
| ATOM 105 C ALA 11 -8.353 -0.574 1.259 1.00 0.00 | ||
| ATOM 106 O ALA 11 -9.466 -0.049 1.310 1.00 0.00 | ||
| ATOM 107 N NH2 12 -8.107 -1.516 0.354 1.00 0.00 | ||
| ATOM 108 HN1 NH2 12 -7.197 -1.950 0.308 1.00 0.00 | ||
| ATOM 109 HN2 NH2 12 -8.840 -1.786 -0.282 1.00 0.00 | ||
| TER |
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