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虽然看不出来你的这个分子是怎么摆的，但是能确定 MD 过程中，重合的是 1-5 位的氮和氢原子。
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看以下这篇文献：https://doi.org/10.1002/jcc.20090：A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
具体的解释牵涉到力场的开发和非键能的计算。
其中的引用是：
In principle, all atom pairs should be included in this sum, but generally, the sum is restricted to a subset of atom pairs. First, covalently bound neighboring atoms (first neighbors) and second neighbors are standardly excluded from this sum. They are already directly interacting through the bonded interactions, and are thus considered to be excluded atom pairs for the nonbonded interactions. In addition, the third or 1– 4 covalently bound neighbor atoms that are part of or bound to aromatic rings are also excluded from the nonbonded interactions. This makes it easier for the improper dihedral angle interactions to keep the atoms of and bound to a planar aromatic ring in one plane. Furthermore, there are a few exceptions to this general rule. These involve hydrogen atoms that have a repulsive van der Waals interaction equal to zero. In cases where the hydrogen is in a 1– 4 or 1–5 covalently bound neighbor position to an oppositely charged atom, X45, and the heavy atom, X1, to which the hydrogen is bonded is an excluded atom with respect to atom X45 an additional exclusion of the hydrogen with atom X45 is sometimes needed. This is because the bonded interactions may fail to prevent the hydrogen atom from collapsing onto atom X45. For example, in the nucleotide adenosine atoms H61 and H62 are excluded from atom N7 for this reason.
所以，很好的一种解决方式是，你在 top 文件里额外添加 `[exclusions] ` (用对应的原子序号），把这个 LJ 为零的氢和和氮之间的非键相互左右给排除掉就可以了。
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发表于 Post on 2023-7-5 15:14:54
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发表于 Post on 2023-7-6 10:43:35
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