GROMACS simulation error while running in collab

[Shrikirti Anand 21PHD0252]

Hello all!

I am trying to run protein-protein simulations in collab pro using GROMACS. I am getting errors like 'Fatal error: XTC error' and 'IOPub data rate exceeded' error. Any help regarding this will be appreciated. I have attached the screenshots for your reference.

thank you

Disclaimer:
This message was sent from Vellore Institute of Technology.  The contents of this email may contain legally protected confidential or privileged information of “Vellore Institute of Technology”.  If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.

[Richard Gowers]

Hi

Welcome to the mailing list.

It looks like your questions aren't about MDAnalysis, but I'll try and answer.  The first message about IOPub is that the notebook is trying to print too much output to screen.  The second error is that there isn't enough disk space for the simulation output, likely because you're running on colab which isn't designed for running gromacs jobs.

Richard

--
You received this message because you are subscribed to the Google Groups "MDnalysis discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to mdnalysis-discus...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/ea3b3aaf-8ea8-4845-94ef-6f2ce207cdbfn%40googlegroups.com.

[Shrikirti Anand 21PHD0252]

Thank you for the answers, sir. Is there any way I can rectify them? 

To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/CAFk3ehny8xaiNDRO_vQCk8aFB-4Q3P7XT0pe8FzN2tb7T6GMOQ%40mail.gmail.com.

[Richard Gowers]

If you want to run a gromacs simulation, you won't be able to do this in colab.

Richard

To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/CACjekdrset1u6VcpESkQTtjQA%3DaiALniay_9XVXAdnfKP7g6EQ%40mail.gmail.com.

[Shrikirti Anand 21PHD0252]

Can you kindly suggest me a method to do so? I was running the gromans package in collab pro because it takes less time to run as compared to running on a system. Is there any other way to run protein-protein simulations? 

To view this discussion on the web visit https://groups.google.com/d/msgid/mdnalysis-discussion/CAFk3ehm%2BeaVftkK3epFQVojYw8RVt-2U1FupvHKp4EGj6fGDUQ%40mail.gmail.com.