CABS-flex server for fast simulation of protein structure fluctuations: http://biocomp.chem.uw.edu.pl/CABSflex/about.php
Many academic institutions have a 'supercomputer' center. There are also organizations (e.g., Metacentrum in the Czech Republic) that allow access by affiliated institutions to shared computational resources (with ready-to-use software, including various molecular dynamics simulation packages), but to get an access, you must be a member of an affiliated institution or have a collaboration with a member.
https://www.metacentrum.cz/en/index.html
One could use CHARMM GUI to generate the system and topology. Then MD simulation can be performed on a local machine or on super-computing facilities whichever the person can afford.
http://www.charmm-gui.org/
As far as I know, there are only free computers online. I think you can run MD simulations on them.
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