Refactor RAMD group initialization to use vector resizing

set pull coord dim, vec, and eGeom

… log-file

add mdp description to README

add backbone and carbon_not_backbone

…eedToCalcCom will be used

by general binding groups

This reverts commit 022ed97.

by calling process_pull_groups after add_residence_time_groups

…pNames for validation

…oid unneeded calculations

…d missing dependencies, compilers and vscode user