fix issue 285

[fgrunewald]

@csbrasnett this is a clean PR with all changes we did yesterday. I also fixed the template generation issue. Can you test this branch?

To Do

• add test for volume computation
• make sure IDP parameters are correct
• add citation to IDP paper
• add warning to include new martini itp file??
• write user tutorial

[csbrasnett]

Bonded parameters look good on testing, but the VS-BB exclusions don't seem to be generated at all?

for generating coordinates the molecule checking fails too, error of two disjointed parts

[fgrunewald]

@csbrasnett I fixed the exclusions. For the structure coordinate generation works though? Can you make a example available to me.

[csbrasnett]

Looks to work now

[fgrunewald]

@csbrasnett the peprint is already out. Are these parameters up to date? Can we merge and release it?

Also can you add the citation to the preprint paper?

[fgrunewald]

One small nitpick about the minimizer, the rest looks fine.

However, it seems @pckroon needs to approve this PR.