MDWeb was tested for proteins with less than 20000 heavy atoms. We started to find some incompatibilities with programs used in the pre-configured workflows with larger systems. Another reason is that being a web server, it had to be restrained in the simulation length and system size.
That said, you can try to use MDWeb2, which is a version of MDWeb with added functionalities and less restrictions. But please note that this is an unstable version.
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!