Crypto-paid MD-Simulations using GROMACS

Site feedback
1

I came across this site while surfing reddit, and thought it would be a good idea to alert the developers here as they are potentially making money off a free to use software.

2

Hello,

thanks for pointing this out. As GROMACS is licenced under LGPL they are legally free to do that.

I just hope people will use established distributed computing projects such as Folding @ Home instead of paying for something like this.

Cheers

Paul

3

Hello everyone,

my name is Thomas Rogg from Neonious.

I am sorry to offend, but I am not really sure why. We are trying to build a cheaper alternative for researchers to scale MD sims (not large MD simulations, but many variations), than using super computers or the cloud. Yes, we are a company, but so is Amazon AWS or others.

Folding@Home is technically not really an alternative - MD sims go much futher than protein foldings, as most of you I guess know. We want to help simulate protein protein interactions and more.

Can anybody give me insights what’s wrong with trying to build a technical infrastructure for GROMACS users?

Thomas

4

Second note, just in case Folding@Home expanded to more than just Folding - not sure. I thought they have their own agenda - right now COVID-19 drugs. Can research groups ask them to calculate their MD sims for them?

This really is not the same topic.

5

@NeoniousTR In the interest of users who may choose to rely on your services, please make sure to:

  • Always distribute a recent versions of GROMACS (latest patch release and only supported major releases);
  • If you make any code modification, please tag the version accordingly. Reproducibility is important (also we do need to know if user reports come in with modified versions of GROMACS); see Installation guide — GROMACS 2021.2 documentation
6

@pszliard
Thank you for the constructive remark.

We plan to use releases, not the master.

We have a few changes in our testing right now, but I think we might be able to get them removed and work with the vanilla version (just linked together instead of using gmx). If we keep changes, we will tag the version strings. Also, we will put the modified version in our GitHub (if applicable, as said).

Thank you.

Thomas

7

Hello @NeoniousTR,

I don’t have any objections to your company providing this service, I’m more concerned (as @pszilard pointed out) that you need to make it very clear to users what version is in use and what kind of modifications (if any) have been applied to the code to work with your infrastructure.

GROMACS has worked together with F@H for a long time to make sure things work right there, and my worries are that you might run into bugs that we haven’t encountered before and we then get asked why the simulations didn’t work, and why your customers had to spend the money for them :)

Please feel free to join us for the next developer teleconference at the end of the month if you want to discuss how to upstream changes you had to make (if this makes sense to you).

Cheers

Paul