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10个受体Y6,2000个溶剂分子。先能量最小化,按照dy-npt.mdp先平衡30n是,再按照 λ=0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00平衡2ns,命令行gmx bar -f md-*.xvg -b 1900 -o bar_results.xvg -oi bar_int.xvg -oh bar_hist.xvg输出结果
Detailed results in kT (see help for explanation):
lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/-
0 1 -272.07 0.61 11.34 0.28 187.41 1.48 25.09 1.16
1 2 -440.54 1.18 17.80 0.81 690.85 1.70 50.02 1.94
2 3 -906.71 1.54 -53.48 0.97 -290.93 1.36 156014528.45 7647697.46
3 4 -495.94 0.49 12.73 0.54 296.24 1.27 27.17 1.73
4 5 -496.72 1.13 11.11 1.36 11.25 0.87 7.97 1.68
5 6 -108.31 1.06 19.04 1.98 53.83 1.43 50.51 1.67
6 7 236.13 0.32 140.20 1.35 137.24 0.57 466964257839805244251308032.00 1516076403662126709601206272.00
7 8 514.94 2.52 -31.62 2.15 -200.73 2.95 60.70 1.48
8 9 1181.31 1.95 354.26 3.35 342.78 2.80 5716792558421376573856712818153600887592179769037529302712495112192.00 52788563421184399531582118199565905663974988866142271021076473136021504.00
9 10 812.91 2.70 758.08 5.30 725.72 2.87 39639538688520239283873617945214995102474991474502967683328327205282704281504393837519704494845341457868712931203065999390428826582414108930396464873472.00 -nan
10 11 116.92 2.00 133.31 6.05 113.97 3.61 149814116281954959360.00 50891591938264730173440.00
11 12 35.67 1.86 70.85 1.92 58.52 1.83 38897252.10 2306728074.01
12 13 13.81 1.27 46.30 2.90 50.55 1.80 2512.41 434456.38
13 14 0.89 1.74 33.08 0.99 45.81 2.25 79.36 1.93
14 15 -11.24 2.20 31.11 1.53 38.14 1.96 65.42 2.25
15 16 -16.71 1.46 27.86 1.17 34.99 1.43 40.51 2.51
16 17 -20.54 0.99 29.96 1.73 31.72 1.13 64.05 3.09
17 18 -14.89 1.45 29.77 1.54 34.46 2.04 54.57 4.09
18 19 -7.52 2.44 41.95 1.64 39.41 2.44 80.52 3.60
19 20 18.31 2.69 79.33 3.74 68.48 2.77 981.21 86.30
WARNING: Some of these results violate the Second Law of Thermodynamics:
This is can be the result of severe undersampling, or (more likely)
there is something wrong with the simulations.
Final results in kJ/mol:
point 0 - 1, DG -678.64 +/- 1.52
point 1 - 2, DG -1098.84 +/- 2.94
point 2 - 3, DG -2261.65 +/- 3.83
point 3 - 4, DG -1237.03 +/- 1.22
point 4 - 5, DG -1238.99 +/- 2.83
point 5 - 6, DG -270.17 +/- 2.64
point 6 - 7, DG 589.00 +/- 0.79
point 7 - 8, DG 1284.44 +/- 6.27
point 8 - 9, DG 2946.58 +/- 4.86
point 9 - 10, DG 2027.67 +/- 6.72
point 10 - 11, DG 291.65 +/- 4.99
point 11 - 12, DG 88.97 +/- 4.65
point 12 - 13, DG 34.45 +/- 3.17
point 13 - 14, DG 2.21 +/- 4.35
point 14 - 15, DG -28.03 +/- 5.48
point 15 - 16, DG -41.69 +/- 3.63
point 16 - 17, DG -51.22 +/- 2.47
point 17 - 18, DG -37.14 +/- 3.61
point 18 - 19, DG -18.76 +/- 6.09
point 19 - 20, DG 45.67 +/- 6.72
total 0 - 20, DG 348.47 +/- 23.20
正常吗,如何修改使得结果稳定
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dy-npt.mdp
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minim.mdp
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Y6-0.mdp
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Y6-1.mdp
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Y6-2.mdp
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Y6-3.mdp
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Y6-4.mdp
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Y6-5.mdp
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Y6-6.mdp
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Y6-7.mdp
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Y6-8.mdp
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Y6-9.mdp
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Y6-10.mdp
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Y6-11.mdp
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Y6-12.mdp
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Y6-13.mdp
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Y6-14.mdp
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Y6-15.mdp
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Y6-16.mdp
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Y6-17.mdp
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Y6-18.mdp
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Y6-19.mdp
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Y6-20.mdp
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