Dear Biomolecular Explorer


Many thanks for your curiosity about biomolecular dynamics. We hope that you find our trajectories enlightening and rewarding!

  1. Please download the compressed trajectory file. You will find these below.

    Tips: These will have been stored for you in a format that can be uncompressed (.zip, .tar, .tar.gz, .tar.xz, etc) with a free program such as 7zip. You will have at least two files: a topology file (small), that specifies the atomic bonding and connectivity within the molecule, and a trajectory file (large), that shows how the coordinates of the atoms change during the dynamics of the simulation.

    The benefactor may have included extra optional information, such as a licence file, and a readme file. The latter will contain extra information that the creators of the trajectory wanted you to know, such as how they performed the simulations.

  2. Load your structure into VMD and enjoy!!

    Tips: To view your trajectories, you will need to take note of where the trajectory files you downloaded are stored you on your computer, so that you can tell VMD where to find them when you read them in.

    Load the topology file (the small file) into VMD first. Then load in the trajectory (that’s going to be the big one!). You should see your molecule dance!! Do have fun playing around with the wonderful molecular representations that VMD provides. There is a CCPBioSim VMD tutorial available here.

  3. Please share your insights and cite the trajectories.

    Biomolecular simulations are extremely computationally expensive, and so consume lots of energy when they run. We therefore need to make best use of them to respect our environment, so please do share and cite! If you'd like to help us build this, then you can submit trajectories here.

    If you have feedback on slimMD, such as how easy (or not!) it is to use, suggestions for improvements or fabulous examples for how you have recycled the trajectories that you would like to share (e.g. how you have used slimMD for teaching), please fill out our feedback form.

    If you have requests for particular trajectories that you would like to see in the slilmMD database, we can circulate to the wider biomolecular simulation community. Please submit your trajectories requests here. We will circulate a list of requested trajectories once a month to our community mailing list.

 

This database of molecular dynamics trajectories has been designed to provide a light-weight set of trajectories for use in training and teaching materials. All MD trajectories in this database will have a simplified description, have a maximum file size of 1GB and will all have been tested and known to work with a vanilla install of VMD.