atoms overlapping

As far as I know, pair style buck/coul/long potential tends to infinity as pair separation length goes to zero, therefor while minimization the close atoms must be attracted to each other and overlap. I think you should use a repulsive potential for close pair separation lengths.

Reference the following literature, There they have used BKS (literally the buck/coul/long pair style) potential for simulate silica structures. they have added a 24/6 lj potential to have the repulsive part in the potential at close pair separation lengths to avid negative infinity issue of the buck/coul/long style.

https://doi.org/10.1016/j.ijheatmasstransfer.2003.11.009

Hope this helps.

Thank you all for the advice. I add a repulsive potential for close pair separation lengths,and it works.

Thanks,

Wu Minbo