标题: 用2019.6 版本gromacs进行拉动C60球和蛋白相互碰撞的仿真报错 [打印本页] 作者Author: MrWang 时间: 2021-4-28 11:01 标题: 用2019.6 版本gromacs进行拉动C60球和蛋白相互碰撞的仿真报错 ; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = C60
pull_group2_name = Chain_A
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N Y N
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
ERROR 1 [file md_pull.mdp]:
When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5 times half the box size a centrally
placed atom should be chosen as pbcatom. Pull group 2 is larger than that
and does not have a specific atom selected as reference atom.