fixing and updating link to third-party in user-guide and how-to pages
Working in user guide and how-to of manual.gromacs.org on updating third party link.
- Link and connect text to PRODGR and MKTOP tools have been removed.
- not-up-to-date tutorials have been replaced with new tutorial link.
- broken link for MDtraj, Swiss PDC viewer have been fixed
- broken link for ROCm (https://rocm.github.io/ broken ) have been replace with https://rocm.docs.amd.com/en/latest/
link to issue #4935 (closed)