GROMACS NPT simulation error after running for 3-4 days

Dear MDWeb,

I had set up a GROMACS NPT simulation and it was running for 3-4 days but never finished. Instead, it gave me the error sign. When I checked the log file it gave a massive list but I dont seem to be able to find what the problem was (apart from “Service Failure. Workflow Stopped, see program log files”).

Is there a way that someone can help me identify the issue? Below is a link to the log file in case is useful.

MDWeb. Molecular Dynamics on Web. f01.moby (

I would be very grateful if you could help me.


Dear Dimitris,

it is difficult for us to identify the issue, as the project is not in your workspace anymore. I have identified a couple of GROMACS NPT runs from the dates you suggest, one failed because reached our servers wall-clock time, and the other succeeded. Could you please confirm that you were finally able to run your short NPT simulation?

Thanks for your interest in our tools and please don’t forget to check the new BioBB-Wfs platform, it might be interesting for your projects.

Best regards,


Dear Adam,

Thank you very much for your reply and time, and in general for all the support to people like me, it’s fantastic!

Yeah, I removed the project to free up space in my workspace. It’s true what you said, one failed and the other one succeeded. Although there are some differences between the complexes in those two, the fact that one worked is already good enough.

I’m facing another other issues now so I hope you don’t mind to take the opportunity to ask for your help.

  • As I mentioned, I deleted some of the project to free up space. Then I wanted to upload one of the projects again but I am stuck in a “loop” and cant’ get past it. I initially type the project title, the select “Upload past MDWeb project”, then I choose the project (which I had downloaded from the MDWeb workspace) in the “Upload project” section and hit “Create project”. I then get a message on the browser that this might take several minutes and the page starts loading. The weird thing is that when the loading stops, the project is not uploaded but instead I get an error saying “Project title is required” (???). And that’s the “loop” as I have to do all the steps described above.

Any idea what might be going on wrong or what I am doing wrong?




Hi Dimitris,

sorry for the late reply, we have been dealing with technical issues with the backend infrastructure these last days.

I could not reproduce your error. I have downloaded a project and uploaded it again, and all seems to work fine. Could you please try it again, just to be sure that it was not a problem of the mentioned technical problems?

Thank you very much for your interest in our tools.