Dear Biomolecular Simulation Philanthropist

 

Many thanks for your kind donation of your valuable simulation trajectories to our slimMD repository for non-specialists.

We advise that donated trajectories should be associated with a peer-reviewed published paper, so that benefactors gain full recognition for their simulations. We will request citation information along with your slimMD submission.

To ensure our users get the full enjoyment from your simulations, we respectfully request that you follow the slimMD etiquette:

 

Yes Please!!
VMD Compatible Filenames Neatly Packed Trajectory and Topology Files
slimmd blocks slimmd packing
No Thanks!!
Enormous Files Unfitted Simulation Trajectories
slimmd munch slimmd sim

 

  1. Please use file-name extensions for your topology and trajectory files that are recognised automatically by the Windows version of the molecular visualisation program VMD.

    Tips: In case you don’t have VMD it can be downloaded here.

    Beware that the Windows VMD release has limited functionality compared to Linux versions, for example netcdf files are not recognised. To be safe, we recommended testing your trajectory visualisation in a Windows environment, if this is available to you.

  2. Please compress your topology and trajectory file (with optional licence and/or readme files) into a single file that can be uncompressed in windows (e.g. file.tar, file.zip, file.gz or file.tar.gz) for upload to slimMD.

  3. Please ensure that your trajectories do not exceed 1GB in size.

    Tips: If you have long trajectories, then please sample infrequently to capture the full dynamics in a compressed form. If you have large systems, don’t worry, even a small number of snapshots can reveal exciting dynamics. Less is more!

  4. Please ensure that trajectories are rms-fitted to remove translation and rotation, and that they are correctly “imaged” into the central periodic box.

    Tips: Most simulations should have water molecules removed from the trajectory. In some instances, it may be instructive to keep structural solvent molecules and/or counterions, and for membrane proteins the lipids are often of interest. Please make sure that these are imaged correctly before submitting your trajectory. This will really help our users to understand your work!