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gwdavid木虫 (著名写手)
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【求助】请帮忙解释一段关于分子动力学的英文！
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If the ligand poses predicted by docking is in the binding pocket determined by the PMF, then the downward slope would ensure a quick convergence of this initial configuration to the actual one in MD simulations. The binding free energies determined from MD simulations will also provide a check on the accuracy of those obtained from docking. 这段话是文献上的，是说用分子动力学优化autodock给出的对接结果，我不太明白。主要是上面两个标红的地方，PMF是什么，它能算结合自由能？分子动力学软件gromacs在模拟这样的受配体复合物时，也能计算其结合自由能吗？请帮忙！ [ Last edited by lei0736 on 2009-11-13 at 21:37 ] |
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2楼2008-12-01 13:54:59
3楼2008-12-01 16:52:14
gwdavid
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4楼2008-12-01 19:40:42
5楼2008-12-02 00:38:40
xuefei06
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gwdavid(金币+1,VIP+0):呵呵，相同的答案，还是谢谢您 ！
gwdavid(金币+1,VIP+0):呵呵，相同的答案，还是谢谢您 ！
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When the system is in a solvent, the PMF incorporates solvent effects as well as the intrinsic interaction between the two particles. When the same two particles were brought together in the gas phase, the free energy would simply be the pair potential , which has only a single minimum. But the PMF between two particles in liquid oscillates with maximum and minimum. For a given separation between the two molecules, the PMF describes an average over all the conformations of the surrounding solvent molecules. Various methods have been proposed for calculating potentials of mean force. The simplest representation of the PMF is to use the separation between two particles as the reaction coordinate. The PMF is related to the radial distribution function using the following expression for the Helmholtz free energy A(r)=-KbTlng(r)+const |
6楼2008-12-03 00:00:32