Okumura Hisashi, Okamoto Yuko
Department of Physics, School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.
J Phys Chem B. 2008 Sep 25;112(38):12038-49. doi: 10.1021/jp712109q. Epub 2008 Aug 30.
We applied the multibaric-multithermal (MUBATH) molecular dynamics (MD) algorithm to an alanine dipeptide in explicit water. The MUBATH MD simulation covered a wide range of conformational space and sampled the states of PII, C5, alphaR, alphaP, alphaL, and C7(ax). On the other hand, the conventional isobaric-isothermal simulation was trapped in local-minimum free-energy states and sampled only a few of them. We calculated the partial molar enthalpy difference DeltaH and partial molar volume difference DeltaV among these states by the MUBATH simulation using the AMBER parm99 and AMBER parm96 force fields and two sets of initial conditions. We compared these results with those from Raman spectroscopy experiments. The Raman spectroscopy data of DeltaH for the C5 state against the PII state agreed with both MUBATH data with the AMBER parm96 and parm99 force fields. The partial molar enthalpy difference DeltaH for the alphaR state and the partial molar volume difference DeltaV for the C5 state by the Raman spectroscopy agreed with those for the AMBER parm96 force field. On the other hand, DeltaV for the alphaR state by the Raman spectroscopy was consistent with our AMBER-parm99 force-field result. All the experimental results fall between those of simulations using AMBER parm96 and parm99 force fields, suggesting that the ideal force-field parameters lie between those of AMBER parm96 and parm99.
我们将多压力-多温度（MUBATH）分子动力学（MD）算法应用于处于显式水环境中的丙氨酸二肽。MUBATH MD模拟覆盖了广泛的构象空间，并对PII、C5、αR、αP、αL和C7(ax)状态进行了采样。另一方面，传统的等压-等温模拟被困在局部最小自由能状态，只对其中少数状态进行了采样。我们使用AMBER parm99和AMBER parm96力场以及两组初始条件，通过MUBATH模拟计算了这些状态之间的偏摩尔焓差ΔH和偏摩尔体积差ΔV。我们将这些结果与拉曼光谱实验结果进行了比较。C5状态相对于PII状态的ΔH的拉曼光谱数据与使用AMBER parm96和parm99力场的MUBATH数据均相符。拉曼光谱得到的αR状态的偏摩尔焓差ΔH和C5状态的偏摩尔体积差ΔV与AMBER parm96力场的结果相符。另一方面，拉曼光谱得到的αR状态的ΔV与我们使用AMBER-parm99力场的结果一致。所有实验结果都落在使用AMBER parm96和parm99力场的模拟结果之间，这表明理想的力场参数介于AMBER parm96和parm99之间。
