MolPlay Frequently Asked Questions (F.A.Q.)

Currently the following issues were identified and will be addressed in future releases:

• bootability in UEFI BIOS mode (see detailed description below)
• small size of the mouse pointer
• internal (laptop) keyboard not working on some Macbook laptop models (workaround: a plugged in USB-keyboard works fine)

Assuming the image was properly downloaded and burned onto the USB stick, booting may fail on your computer due to it’s BIOS (firmware) settings. In principle there are two modes to boot from a USB stick: in Legacy mode or in UEFI mode. Which mode your computer uses is determined in it’s BIOS, with newer computers typically only offering UEFI mode. We plan to release MolPlay images that boot both in Legacy and in UEFI mode.

If your USB stick does not boot and your computer has the BIOS option to do so, try Legacy mode, which has shown to be more failsafe in our experiments.

Note that the current v1.0 MolPlay USB image from 9.7.2024 does not properly boot from UEFI mode, which will be corrected in the next release.

Long-term sustainability is an important issue: many software ideas have had a limited lifetime as continued support did fail sooner or later. How do we plan to keep MolPlay alive and healthy?

• The MolPlay design mitigates this issue to some degree: Batocera has long been supported by a very active community and forms the core of MolPlay. Guix is also a thriving Linux ecosystem. What needs to be added is a relatively thin layer of interactive simulation, visualization and analysis on top. Some elements, such as Gromacs, are very much alive and will certainly remain so for quite some time.
• The part that definitely needs to be maintained concerns the input files for simulation and visualization, the documentation and the user interface.
• The current plan for further support is based on several pillars:
  • First, my own use of MolPlay and that of my lab will ensure support for the next few years. MolPlay makes my IMSA-related activities much easier compared to the way I have been handling them, and I am going to redesign my entire IMSA demo and tutorial stack to incorporate MolPlay for myself because it makes demos, classes and workshops so much easier.
  • The second pillar will hopefully be the MolPlay community that I want to build. Since MolPlay is accessible for everyone to create variants or add their own things, maybe improvements and bug fixes will come naturally. I hope to get relevant groups to collaborate in this field. The Emulationstation front-end allows for a menu/submenu system, so each contributing group could create their own “page” in MolPlay, which could be very useful for their outreach and dissemination.
  • I plan to expand the project not only to IMSA, but to other applications based on the same base “image”, so that the user community and interest could continue to grow, as well as the number of volunteers who could help keep MolPlay alive and up to date.

Very large and complicated systems may, particularly in real-time applications, demand much CPU/GPU resources and running from the MolPlay USB stick can become a performance bottle neck. Such performance issues in scientific applications can be addressed thanks to the modular nature of the coupling between different elements of the interactive simulations.

The coupling between simulation and visualization takes place via the network. The critical part is usually the simulation. With the input files provided on the MolPlay USB stick, it can easily be run on another, more powerful machine (or a compute cluster), and then the visualization running from the MolPlay USB stick “only” needs to be given the network IP address of that machine instead of the default 127.0.0.1 localhost address, e.g. the identical machine from which the USB stick was booted.

Performance needs can also be the other way around, e.g. if you want to connect to an interactive MolPlay simulation from a VR headset (which is currently only supported on Windows), then you would “only” start UnityMol-VR on Windows - with almost exactly the same inputs as provided on the MolPlay USB stick - and connect to the simulation running from MolPlay. Technically this is not difficult and already doable.

In the future I will add video walkthroughs for such scenarios on this website and on the related Youtube channel.

GPU support is in principle provided by the Batocera base system, but this has not yet been thoroughly tested and may require some user configuration to ensure that the appropriate GPU driver is used. This issue will be addressed in the future.