Fix #236

[lohedges]

This PR closes #236 by restricting the loop over the start_indexes vector to the number of molecules in the system.

Also closes #238 by fixing the calculation of delta^2 used in the Coulomb term of the nonbonded expressions.

Also closes #239 by excluding to/from ghost interactions from the ghost_14ff.

Also closes #230 by adding a crude timeout to the OpenMM minimiser. This just checks to see if a maximum number of seconds has been exceeded in both the inner and outer loops of the code. This obviously doesn't check the timing within the internal line search algorithm itself. The main point of this is allow the user a single lever to control the max time (roughly) before the minimiser exits, rather than needing to adjust the number of iterations, ratchets, etc. (And even then, those might still lead to a hang.)

Also closes #241 by re-computing the energy after performing the final constraint projection in order to get the correct delta energy.

Also closes #242 by clearing the internal OpenMM state of the dynamics object when performing a minimisation.

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

[mb2055]

👍 All good (once the CI is done)