GROMACS version: 2020.6
GROMACS modification: Yes/No
Suppose there are two groups A and B. The centre of mass of each group is defined and the distance among them is denoted by d. Each group is pulled along the direction that is specified by
pull-coord?-geometry = distance. By default, steered MD stops if d > L/2 where L is a side length of a periodic box. To avoid this, one possible solution is to increase the box size, but we usually don’t want to because the computation becomes more intense.
Then, how would you avoid the case that an SMD stops if d > L/2? Would there be possible solutions?