query related to my project-> dashboard for tracking MD simulation progress with new streaming interface.

[katala-sanjana]

Hello, I am sanjana. I am a computer science graduate. This is my first time participating in an open source contribution program. I went through the documentation, terminologies, how to set up MD analysis and IMDclient in jupyter notebook, understand trajectory and frames at various stages of atom simulation.

What i learnt is, based on the atom the user chooses(for which we should use select_atoms function), there are various features based on which we can provide insights to the user -> such as calculating distance between atoms, calculating the angle between them, comparing them with previous and current simulations which could give the idea how molecules binding or diverging from the receptor, atom collisions which we can show on the dashboard and we connect to the simulations using this protocol called as IMDv3(intermolecular binding version 3) which is implemented as imdread in MD analysis.

But i have a doubt, if you could clarify it, it would be of great help to me -> for me to do this project, I require simulations right for recording trajectories, so should i write mock simulations or is there any predefined set of available simulations(like dataset for a machine learning model) which we should connect using IMDv3?

Looking forward to hear from you -> Nilay@nilay-v3rma
Amru@amruthesht

[orbeckst]

@amruthesht can you please provide some suggestions for how to get started setting up streaming?

[amruthesht]

@katala-sanjana, this repository on our IMDv3 streaming workshop from last year can be a useful resource on getting started with a MD simulation+streaming setup. The instructions suggest using the pre-configured GH codespace (with GROMACS) for the workshop, which you can try out to familiarize yourself with streaming. However for most practical applications, you would need the simulation engine installed (in some cases, built from source) on your workstation.