用热力学积分的方法计算甲氨蝶呤分子在水中的溶剂化自由能,在md采样时候报错,报错内容如下:
There are 1 perturbed non-bonded pair interactions beyond the pair-list cutoff of 1.219nm, which is not supported. This can happen because the system is unstable or because intra-molecular interactions at long didtances are excluded. If the latter is the case, you can try to increase nstlist or rlist to avoid this. The error is likely triggered by the use of couple-intramol=no and the maximal distance in the decoupled molecule exceeding rlist.
我是用packmol搭建的体系,体系中就一个甲氨蝶呤分子,得到box.pdb,先对盒子进行em、npt、md后,使用md.gro去算溶剂化自由能的。
我选取了21个λ值,第一个λ值能跑完,得到dhdl.xvg, 从第二个λ值开始就报错,设置couple-intramol=yes 也报错,请问一下这是什么原因呀?