MDWeb was designed to help in the first steps of an MD simulation. It eases the not always straightforward setup process, and prepares the needed files to run the simulation. But unfortunately, it is not running a complete MD simulation for you. We don’t have the resources to offer that. What MDWeb offers is a short MD after the setup process (see run tutorial), with a maximum time length of 500ps. This simulation is just a test to ensure that the system has reached a stationary state, after the relaxation done in the equilibration process (included in the setup pipeline). If this equilibration was not enough for the system (it could happen with complex systems), the simulation might crash during the first steps of the “free” MD.
What you can do is follow the run tutorial, fill the parameter fields with a desired time length (for example 10ns as it is done in the tutorial), download the generated configuration files, and run the simulation in your own machine. Note that to assess the stability of a docked structure, you should probably go beyond the 100ns simulation length.
In BioExcel we are trying to update this idea of free MD services 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!