Error that trajectory is larger than 250 MB

[christos-efthymiou]

I am trying to use MDM-Task-Web to analyze my MD simulations for a protein complex, but when I upload my .dcd trajectory, I get an error that the trajectory is larger than 250 MB. I put a step size of 20, and my simulation is only 10 ns. Is there no way to analyze trajectories greater than 250 MB? Is there any way to reduce the size of the trajectory to be able to analyze it on MDM-Task-Web?

[oliserand]

Hi @christos-efthymiou, Unfortunately, we had to impose this size limit for our web server. But you can easily install the tools on your machine using conda, or test out the notebook on binder (bottom icon). The command line application has most features, except for web visualization. The active version of MDM-TASK-web is in the "mdm-task-web" branch. Hope it helps.

[christos-efthymiou]

To clarify, it is not possible to run a local version of the program while having the GUI of the web-server? I was able to download and install the environment using conda, but I am not very familiar with the command line. My simulation files are located on a mapped network drive. Can I use files located on a mapped network drive as an input for these programs? I used NAMD for my simulations so I have pdb, psf, and dcd files available.

[oliserand]

Hi @christos-efthymiou , Dr Mohamed Shehata has a tutorial of how to reduce the size of a trajectory by decreasing the number of frames, in VMD. Maybe you could give it a try and upload the smaller trajectory? Unfortunately, even if there is a URL pointing to the trajectory, it would still need to satisfy the size limitation. Regards.

[christos-efthymiou]

Thank you so much for providing that video, I am now able to use the webserver successfully. Out of curiosity, is it possible to select multiple programs to run on the same trajectory and structure file? For example, I would like to run Communication Propensity, Dynamic Cross Correlation, NMA from MD, and Standard PCA on every simulation I have. Currently, I have to go to each one separately and select my structure and trajectory file and submit the job. As I will be running many simulations, I am looking for any way to speed up the process!

[oliserand]

Hi @christos-efthymiou , we currently don't have plans for that, but it seems to be an interesting idea :-). We'll see if such can be implemented in the future, but no promises.