Wan Shunzhou, Stote Roland H, Karplus Martin
Laboratoire de Chimie Biophysique ISIS (UMR 7006-CNRS), Université Louis Pasteur, 8 allée Gaspard Monge, 67000 Strasbourg, France.
J Chem Phys. 2004 Nov 15;121(19):9539-48. doi: 10.1063/1.1789935.
With the advent of more powerful computers, the question of calculating thermodynamic quantities, such as the energy and the entropy, in solute-solvent systems is revisited. The calculation of these thermodynamic quantitites was limited in the past by their slow convergence relative to the free energy. Using molecular dynamics simulations, the energy, entropy, and free energy of solvation of NMA and CH(3)NH(2), as well as their relative values, have been determined. Three different methods (the thermodynamic perturbation method, the thermodynamic integration method, and a finite-difference method) are compared. The finite difference method gives the best results and accurate values for the entropy and energy were obtained using a reasonable amount to computer time. The results suggest that a meaningful thermodynamic description of biomolecular processes can be realized with present methods and the available computer time.
随着功能更强大的计算机的出现，溶质 - 溶剂系统中诸如能量和熵等热力学量的计算问题被重新审视。过去，这些热力学量的计算因相对于自由能收敛缓慢而受到限制。使用分子动力学模拟，已确定了NMA和CH(3)NH(2)的溶剂化能、熵和自由能及其相对值。比较了三种不同的方法（热力学微扰法、热力学积分法和有限差分法）。有限差分法给出了最佳结果，并且使用合理的计算机时间获得了熵和能量的准确值。结果表明，利用现有方法和可用的计算机时间，可以实现对生物分子过程有意义的热力学描述。
