= 1，会出现Warning: pressure scaling more than 1%及Constraint error in algorithm Lincs的错误，两种...
constraint-algorithm = LINCS tcoupl = V-rescale tc-grps = System tau_t = 0.1 ref_t...
In this article we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm ...
一般被键连的原子间都不计算相互作用(在[ moleculetype ]里定义nrexcl来控制相隔几个键内的原子间不计算相互作用,也就是相当于被列进[ exclusions ]),比如type 1时一般就不计算这两个原子间的非键作用了,而type 2时仍然计算。 用哪种约束算法用.mdp里的constraint_algorithm设定,默认lincs。.mdp里的比如constra...
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Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times ...
constraint-algorithm = LINCS tcoupl = V-rescale tc-grps = System tau_t = 0.1 ref_t...