Yeping Sun, Quoting Justin's answer for a similar question I had on how to repeat a simulation say 10 times " To run 10 independent simulations, I would run minimization once and start from 10 new equilibration runs, each with a different set of initial velocities (change gen_seed or simply set to -1).That approach may not be as robust as starting from 10 different configurations, but the exact approach depends on the system in question".
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