we have a version of MDWeb with added functionalities, one of them being jsmol to avoid the problems you mention. However, it was never functionally tested as MDWeb was, that’s why it was never publicly published as a new stable version. Anyway, if you want to give it a try, this is the URL:
In BioExcel we are trying to update this idea of free MD services (at least setup + configuration files) through GUIs such as web servers. Stay tuned with BioExcel web page or subscribe to our mailing list to hear about the news!
Thanks for using our tools!