How would you avoid the case that an SMD stops if d > L/2?

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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?

Kind regards,

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This is physically impossible, as the distance in a periodic system is not uniquely defined at d>=L/2. And if the distance aligns with a box axis, the largest possible distance is L/2.

The only solution is to use a larger box.

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Thank you very much.
I understand it is impossible.

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direction-periodic

As pull-coord1-geometry=direction , but does not apply periodic box vector corrections to keep the distance within half the box length. This is (only) useful for pushing groups apart by more than half the box length by continuously changing the reference location using a pull rate. With this geometry the box should not be dynamic ( e.g. no pressure scaling) in the pull dimensions and the pull force is not added to the virial.

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I don’t understand the following:

This is (only) useful for pushing groups apart by more than half the box length by continuously changing the reference location using a pull rate.

How can I do “continuously changing the reference location using a pull rate”?
Also, I wonder what the reference location is and why it is needed?

Thanks,

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Hi Natsulait, read this section of the gromacs manual: Non-equilibrium pulling — GROMACS 2021.3 documentation

This answers your question in detail.