Hi everybody,
I have simulated a DNA molecule for about 40ns and after analyzing the
trajectory what I got to know is that the two strands of DNA are going away
( I would say fluctuation of the double helix was observed) for a very
short interval of time and then they are again showing the usual double
helix structure. The backbone RMSD (after re-imaging the trajectory) with
the simulation length was observed as:
0.2 0 0.4 1.4103 0.6 2.6637 0.8 2.9266 1 3.6186 1.2 4.1233 1.4 4.1102
1.6 3.5659 1.8 4.7817 2 5.0723 2.2 5.1966 2.4 5.2689 2.6 4.9271 2.8
5.3689 3 5.0091 3.2 4.9974 3.4 5.4469 3.6 5.592 3.8 6.2973 4 6.3241
4.2 6.1947 4.4 6.318 4.6 6.4998 4.8 6.2249 5 6.4224 5.2 6.2015 5.4
6.4664 5.6 6.3249 5.8 6.2614 6 5.7967 6.2 5.3727 6.4 6.1838 6.6 5.6864
6.8 5.5813 7 5.5123 7.2 5.9466 7.4 6.0938 7.6 6.4089 7.8 6.895 8
6.8932 8.2 7.2321 8.4 7.2644 8.6 6.9741 8.8 6.639 9 5.8916 9.2 5.0106
9.4 5.7208 9.6 5.6487 9.8 5.84 10 5.982 10.2 6.3175 10.4 5.8135 10.6
5.6778 10.8 5.5338 11 4.9699 11.2 4.7924 11.4 5.3463 11.6 6.2329 11.8
5.972 12 5.6154 12.2 6.1696 12.4 5.6921 12.6 5.1745 12.8 5.5655 13
5.5648 13.2 5.9528 13.4 5.8908 13.6 5.9594 13.8 6.0433 14 6.3799 14.2
5.9502 14.4 5.8266 14.6 5.7771 14.8 5.9147 15 5.7344 15.2 5.5604 15.4
4.6345 15.6 4.5849 15.8 4.624 16 4.8061 16.2 4.6168 16.4 4.8163 16.6
5.156 16.8 5.4911 17 5.78 17.2 6.4528 17.4 5.9654 17.6 5.8099 17.8
6.3668 18 7.281 18.2 6.4341 18.4 6.5879 18.6 6.8961 18.8 6.7844 19
6.8823 19.2 7.5653 19.4 7.0299 19.6 6.4855 19.8 6.3822 20 6.3183 20.2
6.6432 20.4 6.3524 20.6 6.5605 20.8 7.0822 21 7.3701 21.2 6.6485 21.4
6.8159 21.6 7.179 21.8 6.8444 22 6.955 22.2 6.5205 22.4 7.2768 22.6
7.0518 22.8 6.781 23 6.832 23.2 6.8739 23.4 7.1469 23.6 6.7654 23.8
6.0378 24 5.3228 24.2 5.874 24.4 5.893 24.6 6.8214 24.8 6.8928 25
5.7248 25.2 6.0796 25.4 5.4216 25.6 5.4974 25.8 6.1135 26 6.8588 26.2
6.9125 26.4 7.5541 26.6 7.139 26.8 7.6506 27 6.9157 27.2 7.9896 27.4
7.3889 27.6 8.0833 27.8 8.3839 28 8.3229 28.2 8.782 28.4 8.7831 28.6
8.4983 28.8 8.472 29 7.4396 29.2 8.3676 29.4 8.501 29.6 8.4742 29.8
8.1767 30 9.1521 30.2 8.6856 30.4 8.6168 30.6 8.6349 30.8 8.2091 31
8.7101 31.2 8.8346 31.4 9.157 31.6 8.8821 31.8 8.9668 32 8.9482 32.2
8.9183 32.4 8.6213 32.6 7.7556 32.8 7.6082 33 6.5383 33.2 6.3985 33.4
6.4741 33.6 6.7054 33.8 5.7364 34 5.6325 34.2 5.0142 34.4 5.3124 34.6
5.5792 34.8 5.1951 35 5.2466 35.2 5.4796 35.4 6.301 35.6 6.5685 35.8
6.7084 36 6.3018 36.2 6.2123 36.4 6.3386 36.6 5.516 36.8 5.4977 37
5.3086 37.2 5.0437 37.4 5.6789 37.6 4.8149 37.8 5.5613 38 5.9093 38.2
5.6627 38.4 5.6125 38.6 5.1466 38.8 5.3554 39 5.9151 39.2 5.6376 39.4
5.3329 39.6 5.6673 39.8 5.9577 40 6.5091 40.2 6.4516 40.4 6.4637 40.6
6.7358 40.8 7.3469 41 7.4628 41.2 6.4069 41.4 6.8132 41.6 6.6913 41.8
6.857 42 7.2237 42.2 7.764 42.4 7.727 42.6 7.2913 42.8 6.8232 43
6.1225 43.2 6.1165 43.4 5.4901 43.6 6.044 43.8 6.4253 44 6.8922 44.2
6.9601 44.4 6.4207 44.6 6.256 44.8 5.6907 45 5.6687 45.2 5.3648 45.4
5.5737 45.6 5.5852 45.8 6.4567 46 5.5783 46.2 6.0409 46.4 5.8916 46.6
5.9613 46.8 6.4089 47 6.1959 47.2 6.732 47.4 7.0554 47.6 7.5075 47.8
6.8631 48 6.7986 48.2 7.5381 48.4 8.7789 48.6 8.6121 48.8 9.212 49
9.8014 49.2 9.6207 49.4 9.4128 49.6 9.1345 49.8 8.8581 50 8.5418 50.2
8.9716 50.4 9.0275 50.6 9.3623 50.8 9.0446 51 7.7847 51.2 7.4903 51.4
7.5193 51.6 6.8708 51.8 7.3663 52 7.0203 52.2 7.4508 52.4 7.3659 52.6
7.6123 52.8 7.1554 53 7.027 53.2 6.086 53.4 6.3398 53.6 6.7312 53.8
6.9075 54 6.8357 54.2 6.1946 54.4 6.9413 54.6 6.8372 54.8 7.3043 55
7.6888 55.2 7.2364 55.4 6.5538 55.6 6.4085 55.8 7.0565 56 6.8003 56.2
7.5421 56.4 6.9248 56.6 6.3975 56.8 6.7775 57 6.6787 57.2 6.4237 57.4
6.6086 57.6 6.5756 57.8 6.3764 58 6.1901 58.2 5.8191 58.4 5.6487 58.6
5.9035 58.8 6.5109 59 6.7774 59.2 7.2012 59.4 7.3156 59.6 7.0035 59.8
6.6923 60 6.6938 60.2 7.5884 60.4 7.2257 60.6 6.6884 60.8 6.676 61
6.2309 61.2 6.1969 61.4 5.7679 61.6 5.3808 61.8 5.8789 62 5.4018 62.2
5.9997 62.4 6.0804 62.6 6.1287 62.8 5.834 63 5.3939 63.2 5.7546 63.4
7.3678 63.6 7.4566 63.8 6.9671 64 6.5727 64.2 7.1732 64.4 6.8287 64.6
6.7315 64.8 7.0345 65 7.0464 65.2 6.8997 65.4 6.5245 65.6 6.1477 65.8
5.4156 66 5.2082 66.2 5.839 66.4 6.4543 66.6 6.7407 66.8 5.6986 67
6.3295 67.2 6.4867 67.4 6.4005 67.6 6.2446 67.8 5.8656 68 5.4533 68.2
6.6034 68.4 6.7698 68.6 6.6516 68.8 5.9443 69 6.3103 69.2 7.2074 69.4
7.4217 69.6 7.4044 69.8 7.2617 70 6.2568 70.2 7.209 70.4 6.7008 70.6
6.7224 70.8 6.8002 71 6.341 71.2 6.8924 71.4 6.201 71.6 6.3671 71.8
6.3288 72 6.3854 72.2 7.2466 72.4 7.8195 72.6 7.2116 72.8 7.6127 73
7.0804 73.2 7.4235 73.4 6.9997 73.6 7.1117 73.8 7.124 74 7.5129 74.2
7.7464 74.4 7.9473 74.6 8.237 74.8 8.0428 75 8.1365 75.2 6.7084 75.4
7.3756 75.6 7.0639 75.8 6.4619 76 6.2582 76.2 5.5545 76.4 5.7611 76.6
6.1419 76.8 5.7708 77 5.5656 77.2 6.3962 77.4 5.8627 77.6 6.6559 77.8
6.3514 78 6.6874 78.2 5.9188 78.4 5.6665 78.6 6.0213 78.8 6.0442 79
6.3586 79.2 6.6988 79.4 6.7806 79.6 7.1677 79.8 7.3512 80 7.5676 80.2
6.8819 80.4 7.0403 80.6 6.5488 80.8 7.1652 81 7.2365 81.2 7.7483 81.4
7.982 81.6 7.7288 81.8 7.683 82 7.9321 82.2 7.2475 82.4 6.8908 82.6
6.2378 82.8 6.4528 83 6.5626 83.2 5.7346 83.4 5.8671 83.6 5.8594 83.8
5.858 84 5.1237 84.2 5.5923 84.4 5.8701 84.6 6.0623 84.8 6.012 85 5.83
85.2 6.3152 85.4 5.9226 85.6 5.8323 85.8 5.7626 86 5.5024 86.2 4.7355
86.4 4.4801 86.6 4.4136 86.8 4.2352 87 3.9724 87.2 4.1877 87.4 4.5563
87.6 4.6356 87.8 5.8235 88 5.5617 88.2 6.019 88.4 5.6793 88.6 5.157
88.8 5.0862 89 5.2612 89.2 4.9114 89.4 5.4819 89.6 5.434 89.8 5.8775
90 5.936 90.2 6.3033 90.4 5.9769 90.6 6.7042 90.8 6.6007 91 5.8689
91.2 5.6683 91.4 5.7092 91.6 5.5558 91.8 5.8739 92 6.9167 92.2 6.2291
92.4 5.9143 92.6 5.9071 92.8 6.6719 93 6.1314 93.2 6.2128 93.4 6.6217
93.6 5.9625 93.8 6.4878 94 6.665 94.2 6.7183 94.4 7.5054 94.6 7.5792
94.8 7.4932 95 7.3632 95.2 6.2692 95.4 5.4967 95.6 5.6958 95.8 5.8236
96 6.1998 96.2 5.5455 96.4 6.5589 96.6 6.7185 96.8 6.9233 97 6.6215
97.2 6.8059 97.4 6.8988 97.6 6.3734 97.8 6.1921 98 6.6811 98.2 6.583
98.4 6.1835 98.6 5.6432 98.8 5.6425 99 5.598 99.2 5.1539 99.4 5.7468
99.6 5.8444 99.8 5.9633 100 5.5719 100.2 5.6996 100.4 5.5214 100.6
5.5084 100.8 5.5679 101 4.7588 101.2 5.0585 101.4 5.3403 101.6 5.7489
101.8 6.2637 102 6.2943 102.2 5.2989 102.4 4.57 102.6 3.9303 102.8
4.379 103 4.1534 103.2 4.0574 103.4 4.1754 103.6 4.8625 103.8 4.9959
104 5.1946 104.2 5.4356 104.4 5.98 104.6 6.5259 104.8 6.6944 105 6.7565
105.2 6.6174 105.4 6.2768 105.6 7.0438 105.8 7.2087 106 7.373 106.2
7.6387 106.4 7.3833 106.6 7.4302 106.8 6.9496 107 6.4307 107.2 5.4413
107.4 5.796 107.6 6.0219 107.8 6.9974 108 7.1818 108.2 6.7283 108.4
7.4835 108.6 7.7628 108.8 7.8478 109 8.0008 109.2 8.0412 109.4 7.9138
109.6 7.6905 109.8 7.4146 110 7.714 110.2 7.8784 110.4 8.1706 110.6
7.8203 110.8 7.278 111 6.3479 111.2 7.0742 111.4 7.8442 111.6 8.1104
111.8 8.6894 112 8.4336 112.2 8.3255 112.4 8.5421 112.6 7.8571 112.8
8.4529 113 8.0793 113.2 7.6486 113.4 7.8165 113.6 7.3091 113.8 7.921
114 8.0833 114.2 8.4221 114.4 7.5545 114.6 7.5328 114.8 7.2655 115
7.4093 115.2 7.8952 115.4 7.7371 115.6 8.083 115.8 8.1266 116 7.446
116.2 7.0122 116.4 7.5337 116.6 7.4308 116.8 6.9517 117 7.226 117.2
6.6205 117.4 7.0966 117.6 7.3582 117.8 7.4163 118 7.2382 118.2 7.0025
118.4 6.4919 118.6 6.824 118.8 7.2238 119 7.2382 119.2 7.8568 119.4
7.6952 119.6 7.5583 119.8 7.1009 120 6.8185 120.2 6.4892 120.4 6.1055
120.6 6.3285 120.8 6.1353 121 5.8272 121.2 5.7965 121.4 5.918 121.6
6.7318 121.8 7.0195 122 6.7448 122.2 6.6371 122.4 7.663 122.6 8.1149
122.8 8.0224 123 8.0669 123.2 8.7158 123.4 8.3917 123.6 8.3803 123.8
7.8962 124 7.1396 124.2 6.1234 124.4 5.8994 124.6 5.5908 124.8 5.5225
125 5.3046 125.2 5.5566 125.4 5.355 125.6 5.9538 125.8 5.4612 126
6.4587 126.2 7.51 126.4 7.1985 126.6 6.9526 126.8 7.1084 127 7.6448
127.2 7.6488 127.4 7.4866 127.6 7.2095 127.8 7.3491 128 7.4631 128.2
7.9699 128.4 7.742 128.6 7.7872 128.8 7.0152 129 6.7252 129.2 5.9054
129.4 5.87 129.6 6.3076 129.8 6.0677 130 5.8141 130.2 5.9016 130.4
5.7556 130.6 5.9932 130.8 6.0662 131 6.4857 131.2 6.6563 131.4 6.499
131.6 6.5614 131.8 6.1777 132 6.3606 132.2 6.8008 132.4 6.8218 132.6
6.5991 132.8 6.9845 133 7.2497 133.2 7.715 133.4 6.6883 133.6 6.4729
133.8 7.1591 134 7.5133 134.2 8.0579 134.4 57.6819 134.6 57.8588 134.8
8.8511 135 9.0555 135.2 8.7235 135.4 57.4898 135.6 8.2367 135.8 7.8345
136 57.2015 136.2 57.3173 136.4 6.685 136.6 6.4999 136.8 57.0807 137
57.3377 137.2 57.1656 137.4 57.803 137.6 57.5671 137.8 7.9082 138
7.6235 138.2 7.109 138.4 6.9595 138.6 8.3329 138.8 7.4766 139 57.4421
139.2 57.3288 139.4 57.3209 139.6 57.746 139.8 7.5531 140 7.5273 140.2
7.2133 140.4 7.9353 140.6 8.8445 140.8 57.998 141 57.8915 141.2 8.4038
141.4 8.6061 141.6 7.8557 141.8 7.2453 142 7.402 142.2 7.5618 142.4
8.0686 142.6 8.3401 142.8 8.2084 143 8.3834 143.2 8.6052 143.4 8.277
143.6 8.8465 143.8 8.8261 144 8.8709 144.2 8.2162 144.4 8.2048 144.6
8.0614 144.8 8.5985 145 8.3709 145.2 8.3152 145.4 9.1746 145.6 9.7987
145.8 8.6049 146 8.1334 146.2 8.0222 146.4 7.8274 146.6 7.8895 146.8
7.5015 147 7.6835 147.2 7.7376 147.4 7.5077 147.6 7.635 147.8 7.6433
148 7.3742 148.2 7.499 148.4 7.0129 148.6 58.1865 148.8 57.7052 149
57.5724 149.2 7.1086 149.4 6.5633 149.6 6.0921 149.8 6.5024 150 6.8033
150.2 7.1799 150.4 7.8425
What could be the possible reason for this fluctuation. Is this fluctuation
indicates that the MD protocol is wrong? Please suggest.
Please let me know if some of the input/output files are required for
solving this problem.
Thanks and Regards,
Jac
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Received on Thu Jun 04 2015 - 07:00:03 PDT
