phase 下之 TI1(remove charges)、TI3(add charges)的部分則僅需 1 條軌跡即可。而 在 solution phase 下，不論是 TI1、TI2、TI3 都只需要在 production run 進行 600ps 即可得到收斂數值。
比較 TTA 與 STA 的部分，單就比較各自之 solution phase 或者是 complex phase 自由能，差異會較大，我們所探討的原因是在於電荷計算上使用到 particle mesh Ewald，Ewald summation 為龐雜的數學計算，在 TTA 與 STA 當中略有不同，因 而導致單獨就 solution phase 或者是 complex phase 之自由能差距較為的大。若將小 分子化合物當中所有原子電荷數值減小，即將電荷效應減小，則可發現單就自由
最後根據先前本實驗室所做出有 Ki 值之兩化合物相對自由能利用 RESP 計算 電荷情況下能夠得到僅僅與實際實驗值相差 1.1kcal/mol 之數值。因此可推論在相 同的結晶結構環境下，以先前作的為基準預測新化合物的誤差值也在此附近，所 以 CFO 相較於 82A 以能量觀點來說；是更為理想抑制 Erk 的分子。
英文專有名詞中文翻譯
1. 蛋白質激酶(protein kinase) 2. 訊息接收者(membrane receptor)
3. 三磷酸腺苷(adenosine triphosphate,ATP) 4. 基因表現(gene expression)
5. 蛋白質失調(deregulation) 6. 過度表達(overexpression) 7. 突變(mutation)
8. 藥物發現(drug discovery) 9. 藥物設計(drug design) 10. 分子嵌合(Docking)
11. 分子動力學模擬(Molecular Dynamics simulation, MD ) 12. 熱力學積分(Thermodynamic Integration, TI)
13. 細胞外信號調節激酶(Extracellular signal-regulated kinases, Erk) 14. 細胞增生(proliferation)
15. 存活(survival) 16. 分化(differentiation) 17. 運動(motility)
18. 酪氨酸激酶 (tyrosine kinase)
19. 核轉錄因子(nuclear transcription factor) 20. 特異性(specificity)
21. 活化位(active site)
22. 活化迴圈(activation loop) 23. 組件(package)
24. 力場(force field) 25. 伸縮(bond stretching) 26. 鍵角(bond angle) 27. 扭角(dihedral angle)
28. 凡得瓦作用力(van der waal’s force)
29. 靜電作用力(electrostatic interactions) 30. 波茲曼分布(Boltzmann distrubution) 31. 時間梯步(time step)
32. 摩擦係數(viscosity coefficient) 33. 高斯分布(Gaussian distribution)。
34. 摩擦係數(viscosity coefficient)
35. 邊界條件(periodic boundary condition ,PBC) 36. 外顯性水模型(explicit solvent)
37. 熱力學循環(Thermodynamic cycle) 38. 起始哈密頓算符(original Hamiltonian) 39. 擾動哈密頓算符(perturbed Hamiltonian) 40. 能量極小化(minimization)
41. 最陡下降法(steepest descent method) 42. 共軛梯度法(conjugate gradient method) 43. 能量相對低點(local minima)
44. 應用變分法(calculus of variations)
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