模拟二氧化硅吸附气体报错

hyq12

求助
用GROMACS模拟二氧化硅吸附甲烷气体，跑完能量最小化之后，跑动力学模拟报错如下，请问这是哪里出错了呢？
甲烷用的amber力场，二氧化硅使用sobtop例子里面的力场，水分子用tip3p力场
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 288 atoms. The longest distance involved in such interactions is
1.869 nm which is above half the box length. Either you have excessively large
distances between atoms in bonded interactions or your system is exploding

sobereva

什么文件都没提供，没法准确判断
反复检查拓扑文件的合理性，确保二氧化硅单独能跑成功再跑加其它分子的情况
记得用periodic-molecules = yes

hyq12

感谢sob老师的回复！periodic-molecules = yes开启了，单独二氧化硅试过了可以跑，但是整体没法跑，文件都在这里能麻烦您帮忙看一眼哪里有问题吗