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最近本人在猛攻gromacs的manual在看前看了几本关于分子模拟入门的书籍，有了一些初步的概念
但是gromacs中的有一些概念，并不是十分清楚。请求高人指点！（问题是基于4.6及以上版本）
Q1：原文：. GROMACS employs a pair list that contains those particle pairs for which non-bonded forces must be calculated. The pair list contains atoms i, a displacement vector for atom i, and all particles j that are within rlist of this particular image of atom i. The list is updated every nstlist steps, where nstlist is typically 10. There is an option to calculate the total non-bonded force on each particle due to all particle in a shell around the list cut-off, i.e. at a distance between rlist and rlistlong. This force is calculated during the pair list update and retained during nstlist steps.
是关于rlistlong和rlist的之间的非键作用力计算。。这里不是很懂原因。为何要每个原子在cut-off附近的总非键作用力？
Q2：第二个问题是关于charge group的。在几本书里都没发现这个概念。根据gromacs的操作手册介绍，应该是在Edwal等长程作用力算法之前的一种计算库伦力的策略。
但是后来就没用了。。想问一下这个概念在实际的算法中是怎么运作的。看了原文后更加晕了。。charge group之间的原子都被列入了pair list中。
原文：Charge groups were originally introduced to reduce cut-off artifacts of Coulomb interactions. When a plain cut-off is used, significant jumps in the potential and forces arise when atoms with (partial) charges move in and out of the cut-off radius. When all chemical moieties have a net charge of zero, these jumps can be reduced by moving groups of atoms with net charge zero, called charge groups, in and out of the neighbor list.there is still an important reason for using “charge groups”: efficiency with the group cut-off scheme. Where applicable, neighbor searching is carried out on the basis of charge groups which are defined in the molecular topology. If the nearest image distance between the geometrical centers of the atoms of two charge groups is less than the cut-off radius, all atom pairs between the charge groups are included in the pair list.
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发表于 2014-12-12 21:16:34
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