xtc | project provides an awesome server | Runtime Evironment library

I use GROMACS. I think about how can I make my script faster. This is my script

I am running the following slurm script on a cluster computing system.

I am entering a command in my bash terminal of the form:

I am running a simple benzene simulation in GROMOS54a7. I want to calculate the RDF of the center of masses of each benzene molecule, using MDAnalysis 1.0.0.

Is this possible? I have create the rdf for the C molecules g_cc(r) using the following code in a Jupyter Notebook:

I would like to know whether it is possible, and how, to host a Jupyter Notebook page somewhere remotely (so not on my machine) that a collaborator could load in their web browser to view results? There is no shared machine, all the files need to be in one central location e.g., hosted on Google Drive, and the Jupyter Notebook page must also be URL based accessible.

First of all, I've performed MD simulations using Gromacs and the files are currently local on my machine. I then load Jupyter Notebook on my machine, import the MDAnalysis Python package and perform some analysis that depends on those trajectory files generated by Gromacs (.trr/.xtc/.pdb). I also include some short simulation trajectories using NGLViewer so I can observe the parts of a simulation.

The problem I face is that I want my collaborator to see/interact with the analysis work and observe the simulations using NGLViewer.

There are a few challenges involved:

(1) How/where do I host a Jupyter Notebook remotely so my collaborator can view progress in a browser window? I'm not expecting them to make edits or run code, just observe and copy text and download figures. This is to save me from packaging (e.g., as a markdown document of some kind) incremental versions of analysis and emailing them over.

(2) What is required for analysis code (written in Python and using the MDAnalysis package) in this remote Jupyter Notebook page to load data files that are stored remotely on e.g., Google Drive?

(3) Similar to (2), can NGLViewer load a remote file e.g., stored on Google Drive, and display the trajectory on the site for the collaborator to observe?

Although my question ties in python packages such as MDAnalysis, NGLViewer and the results from a third party application (Gromacs), I'm looking for a new way sharing results from multiple projects to teams in different countries, along with my own team who I can't meet in person at the moment.

I am currently trying to format a row in a vuetify table (values from an array should be displayed with comma and space using .join()). For this I use a dynamic #item. slot. As long as i don't use join, etc., it works fine. This one works:

I would like to extract one chain from my molecular dynamics trajectory (xtc file) using MDAnalysis. I expected it to be very simple, but an error occurred and I am not sure why I am getting it. Here is the code:

I am trying to follow this post, but it fails to display a PDB inside a Jupyter notebook:

I started to work in the field of computational chemistry and I was ask to do Principal Component Analysis on some trajectory from molecular dynamics. I was told to use MDAnalysis package, thus I find one tutorial on their page a tried to follow it (but I included my own inputs of course) to see if it will be working. I have never done analysis like this ad I am also new to python coding. I attached my code inspired by tutorial. But it doesnt work for me, it raises many errors, one of the errors is that it cant take my inputs (topology is PDB file, coordinate is XTC file), but those are formats which are listed in supported formats or other error is that "class PCA" is not defined. I didnt find much about dealing with PCA using MDAanalysis from other people, thus I hoped that here I could find someone, who have ever done something like this and could, please, help me. I have alreadz tried related subreddits, but without result.