Updated headers for VES

Thanks @hanatok!

Also this after a discussion with @marcodelapierre

thanks to @marcodelapierre

This reverts commit 2128bada.

Giving false positive in master branch - no idea why and cannot debug it

This reverts commit 5ba9eb93.

- when using NAMD-like interface, also update the unique list of atoms.
- moved g2l out of dd, since it is also needed when not using MPI
  (in NAMD-like interface)

Partly implemented by @hanatok, see #359

More efficient on travis-ci

Useful when working with tutorials

I made it more similar to the official one so that it is easy
to see differences

it includes an additional modification to keep multisim in sync when using plumed