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QMMM: update force.c

Kaymak, Cagri requested to merge QMMM_force_update into master

QMMM interface related: ignore QM-MM bonds while forming bond lists, update charge matrix so that the total charge constraint only applies to QM atoms.

Currently, updated matrix works fine for non-periodic simulations but energy fluctuates for periodic simulations

Edited by Kaymak, Cagri

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