Sorry, mistake on my part with the contact email.

Please use hello@molydyn.com if you want to reach out to Matt.

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Apr 13Liked by Tony Maiorana

Overall, I had some critical comments earlier, but I'm going to try to use Molydyn but will need to implement all the LAMMPS stuff which will require figuring out how to set up LAMMPS on Windows. Molydyn figures out where I'm going to get the CPU power from.

I see the potential for a machine I can stuff coins into and it spits out realistic models in a .xyz or .cdx file for structures and a .csv of properties that I can use to get a picture of why a structure has specific properties rather than just handwaving at sterics or electronics or 'VDW forces go brrr'.

I can incorporate that 'less-than-a-blind-guess insight' into tech sales and planning of new product dev. The service as is only gets you the middle part of the process and it could be a tough sell (low value add) to market this service to hardcore comp chemists who are probably have a career/thesis invested in doing it their own specific way.

There is a big overlooked thing here about Molydyn having a foothold to take LAMMPS and MD to the masses where you would have a larger customer base to support doing more cool things. DFT models - for all its criticism - made a splash in quantum models because it was less scary and easier to pick up, it democratized the field though it may have traded some accuracy and 'commoditized' the process a bit (everybody doing wonky DFT calculations in their synthesis paper). But at least it got more people taking about the field than if we were still running pure ab initio calculations.

Also, the Purchase Credits tab is very hard to understand. What's going on here when I put in 1, 10, 100, etc.? One credit = how many dollars. And then there's apparently some free credits for buying specific numbers of credits?

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Apr 11·edited Apr 11Liked by Tony Maiorana

Computational polymer scientist here.

Really cool to see Molydyn's work. However, so far it just seems to set up simulations, which other commercial software already do (even if Molydyn might be a bit newer/more modern). But I think there is still a mismatch between what Molydyn (or any of these commercial software) are trying to sell (simulations for non-experts) vs software that makes experts' life easier.

Another question that is often elided is that running simulations is different from running *good* simulations. Simulations are just computer experiments. For example, many "casual" simulation papers in the literature using currently existing commercial software are often ridiculously short. At some point, it's not so much that the computational resources themselves are expensive, but that the *time* to do quality simulations that give meaningful results is expensive. There is also a lot of polymer theory that goes into properly extrapolating simulations into real-life polymer systems.

If someone here does have experience getting good use out of say, Schrodinger, Biovia, Synopsys, or Siemens' molecular dynamics software, I'd love to hear about how simulation has helped your work. I'm especially interested if you're an experimentalist who has benefited from simulations partnership. My experience is that this usually requires really close partnership between a theorist and experimentalist to find the intersection between what is possible via "in vivo" and "in silico" experiments.

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Apr 11·edited Apr 11Liked by Tony Maiorana

If you're into books and spreadsheets, I love Van Krevelen's 'group contribution' method for predicting properties of polymers but it's not as inspiring as a whole simulation.

The Molydyn UI needs some work. It's a bit too raw to invite a casual user and something close to click/drag interface like Chemdraw would be more approachable to a pure synthesis person looking to get started in simulation. Someone completely new isn't going to know what LAAMPS is or Leonard-Jones potentials, there has to be some hand holding and oversimplification with a JMol kind of input/output for most, and an Advanced Mode for experienced MD users who could enter all the parameters in just a DOS prompt if they wanted.

I should probably watch their tutorial haha. Even Gaussian for DFT or Abalone for MD are easier to hack around in and at least get something wiggling on the screen.

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