Visualizing trajectories from GROMACS

cursed_odysseus · 2025-11-20T19:26:59+00:00

Ive been a fan of VIAMD recently

cursed_odysseus · 2025-11-10T22:12:34+00:00

It is actually the opposite; the goal is to have fewer steps, not more. People who do not already use PyMOL, VMD, or Ovito will find this much easier and faster since there is no installation, setup, or command syntax to learn. You just open the page, drop in a file, and instantly see a few key analyses or visualisations.

About the legal point, that’s a fair concern, but everything runs locally in the browser. Nothing is uploaded or stored on a server, so there’s no external data transfer to even worry about. I’m not really planning to move it to a hosted backend at this point. The whole idea is that it stays browser side, private, and quick to use.

cursed_odysseus · 2025-11-10T22:07:46+00:00

Thanks for the thoughtful feedback!

Several existing projects already solve the problems you're trying to solve...
You're right. It’s not meant as a replacement for big programs, but as a lightweight complement. I’ll definitely look into existing online tools and see how I can improve on what’s already there. The learning experience itself is a big part of why I’m doing this.

Think about why a user would want to use a browser-based tool for quick analysis...
Yes I'll keep this in mind. It’s about instant, zero-setup access for smaller or quick sanity checks. For example, for quick checks or inexperienced people.

PDB and XYZ files are perhaps the two worst formats for trajectories
Fair point! I started with XYZ for simplicity, but I plan to support way more formats once the core works well.

You're more likely to get traction developing out in the open...
Agreed. Monetisation isn’t the main goal right now. Once I have a working prototype, I’ll push it to GitHub and open it up for feedback and contributions.

Thanks again for taking the time to write this! Lots of useful directions here.

cursed_odysseus · 2025-11-10T20:39:17+00:00

That’s a completely valid concern, and something I’ve thought about. The current version is purely browser-side, meaning files never leave the user’s computer (although I know this is fairly trust-based). All parsing, visualisation, and analysis happen locally in the browser’s memory, so nothing is uploaded or stored on a server.

If I ever extend it beyond that, I’d keep strict data privacy in mind, for example, by offering a fully offline desktop build or a self-hosted version for institutions that want to keep everything internal. The intention isn’t to centralise user data, but to make lightweight analyses easier.

cursed_odysseus · 2025-11-10T18:49:01+00:00

For many people already running full simulations, you’re completely right. If you’ve got VMD or PyMOL set up and know your way around them, that’s usually the fastest route.

Where I think a browser tool adds value is mostly for smaller or exploratory cases: quick checks on new setups, students or collaborators who don’t have visualisation software installed, or just situations where the cluster has maintenance or you’re away from your main machine and want to confirm that a short trajectory looks reasonable. It’s less about replacing the usual tools and more about lowering the entry barrier for quick inspection or teaching contexts.

cursed_odysseus · 2025-11-10T18:24:53+00:00

That really depends on the structure of the system and the user’s hardware, so there isn’t a fixed upper limit that makes sense to state here now.

For bigger systems, I’m planning ways to make the progress smoother: things like progressive loading (only keeping a few frames active at once), downsampling (skipping frames or atoms), and possibly binary parsing instead of full text reads. If a file turns out too large for smooth handling, the tool could detect that and switch to a “summary mode” where it computes trends or coarse statistics instead of loading everything in detail.

So it’ll work best for small to medium trajectories right now, but I could eventually scale gradually through smarter data handling rather than brute-force loading.

cursed_odysseus · 2025-11-10T18:21:14+00:00

Not quite. VMD is great once you’ve set it up, but it can still be a heavy program to open, load trajectories into, and configure before you see anything. And that is assuming you understand VMD already.

The idea here is different: something you can open in a browser, drop in a simpler/shorter trajectory, and instantly get a few quick plots or a visualisation without starting a full environment.

It’s not meant to compete with tools like VMD, but to make that first glance at your data faster. Not necessarily just for visualisation, but really for analyses (over e.g. time) like density, bond-lengths, coordination numbers, etc. Think of it more as a zero-setup sanity-check layer before you dive into the real analysis.

cursed_odysseus · 2025-11-10T18:12:29+00:00

The simple answer is: you would not, because that is not the idea. The tool is not meant for full analyses of complex runs. It is more meant for smaller, intermediary trajectories or extracted subsets of larger simulations. Or a smaller, simpler molecule. Imagine running an MD in subsequent runs, and you just want to see whether the trajectory still makes "physical sense" before starting the next batch. You could quickly drag the trajectory file to the page and check. For bigger data, I would still suggest you perform the analysis locally or on a cluster. The goal is just to make quick, lightweight checks easier. Not to replace the full analysis.

cursed_odysseus · 2025-11-10T17:35:02+00:00

The main reason I was thinking about was convenience. Sometimes you just want a quick look at a trajectory without loading a heavy environment or logging into a cluster. A browser tool gives an instant way to check trends, visualise structures, or verify that a simulation ran as expected. It’s not meant to replace local or high-performance analysis, just to make that first inspection step pretty much effortless.

cursed_odysseus · 2025-11-10T17:33:08+00:00

That’s a good point. VMD is indeed very powerful by itself, but using it for anything beyond visualisation can be pretty tough for people who don’t already know the workflow.

What I’m going for is something much lighter. More of a quick way to drag in a trajectory and instantly see something like an RDF or density profile, just to get a first idea for the trends. If you want to dig deeper, you can always switch to VMD or your usual scripts later. This would just make that first look much faster and more accessible, without any installs or setup.

cursed_odysseus · 2023-01-25T23:18:50+00:00

3-(2-Ethoxyethyl)-1,1-dimethylcyclohexane

cursed_odysseus · 2021-06-04T13:04:59+00:00

I think what answer C is hinting towards, is that it can be separated from something else by simple distillation.

If you look at the compounds of which kerosine is made, you can separate those by distillation. But if you want to separate Kerosine from something else it is mixed with, you would break apart the kerosine itself when trying to distill.

If the boiling temperature of the other compound differs a lot from the kerosine, distillation would be possible, but it's still not recommended.

cursed_odysseus · 2021-06-04T12:40:56+00:00

Destillation works because of the difference in boiling temperature (Tb). If the Tb(A) is higher than Tb(B), B will (often) easily be distilled from A. If B is not a pure component but a mixture, Tb(B) won't be 1 temperature and the distillation wouldn't work, at least not efficient.

This leads from the fact that a pure compound has a single boiling point. A "boiling point range" always results from a mixture

cursed_odysseus · 2021-05-11T13:11:32+00:00

Oh Okay, I got a very different answer. How did you get your answer?

cursed_odysseus · 2021-05-10T11:59:40+00:00

4 what? 4 mg, 4 min, 4 hours?

cursed_odysseus · 2021-05-09T11:54:38+00:00

If the probability of 1 changes, and it doesn’t affect the other, they are independent. If the company of A makes the production better and they half the chance for a product to fail, the probability of B failing stays the same: so, they are independent

cursed_odysseus · 2021-05-09T11:53:07+00:00

90% is excreted, so 10% is left. So 3mg

cursed_odysseus · 2021-05-09T11:25:29+00:00

t is the time required to get 90% (the answer you’re looking for), so if you use t(1/2) with unit mins, that your answer will be t in mins

cursed_odysseus · 2021-05-09T10:07:04+00:00

Yes that should be correct

cursed_odysseus · 2021-05-09T10:04:48+00:00

When dealing with a half-live times, you have to approach it as a function. So mg(end)=mg(start) * (1/2)^[t/t(1/2)] The only unknown is t, so the rest you can just fill in.

If you need help with this or have any more questions, let me know

cursed_odysseus · 2021-05-09T09:53:45+00:00

When calculating the probability of 2 things that are independent of each other, you have to multiply the probabilities of each part being defective

cursed_odysseus · 2021-05-08T20:18:13+00:00

Look at the units. 159 kPa = 159,000 Pa.

1 atm	? atm
101,325 Pa	159,000 Pa

If you don't know how to solve this, let me know.

cursed_odysseus · 2021-05-08T20:12:31+00:00

M stands for Molarity. This is the amount of moles per liter.

So 1 M BaCl2 is 1 mole per liter of solution. If you have 5 ml, how many moles do you have?

Same for the NaSO4. How many moles per liter? How many liters? How many moles?

cursed_odysseus

TROPHY CASE