OS error

[ShrikirtiAnand]

I am running a 100ns MD for protein-protein complex (118 aa and 121 aa = 239 aa) in the notebook by taking a Colab pro version. I got an 'OS error: Transport endpoint not connected' after 4 hrs of run. I have put the stride time as 10ns and number of strides as 10. How do I fix it? I have attached a picture for reference.

[pablo-arantes]

HI @ShrikirtiAnand,

Sorry for my delay. I looked into your issue and seems to me this a problem on Google Drive, you can check here: https://github.com/googlecolab/colabtools/issues/3441

My suggestion for you is to perform more strides with less nanoseconds. For example, instead to use 100 of 10ns, you can try 50 strides of 2ns. With that, if the connection is gone you would have save the most part of your MD simulation.

I hope it helps.

Thank you.

Best,

Pablo

[ShrikirtiAnand]

Thank you for the response, Sir. I will try 50 strides of 2 ns. Thank you.

On Sat, Oct 14, 2023 at 11:52 PM Pablo Ricardo Arantes < @.***> wrote:

HI @ShrikirtiAnand https://github.com/ShrikirtiAnand,

Sorry for my delay. I looked into your issue and seems to me this a problem on Google Drive, you can check here: googlecolab/colabtools#3441 https://github.com/googlecolab/colabtools/issues/3441

My suggestion for you is to perform more strides with less nanoseconds. For example, instead to use 100 of 10ns, you can try 50 strides of 2ns. With that, if the connection is gone you would have save the most part of your MD simulation.

I hope it helps.

Thank you.

Best,

Pablo

— Reply to this email directly, view it on GitHub https://github.com/pablo-arantes/making-it-rain/issues/82#issuecomment-1763105458, or unsubscribe https://github.com/notifications/unsubscribe-auth/A74MDGLFRETOTEV475XYEYTX7LJ4XANCNFSM6AAAAAA5VHVRJQ . You are receiving this because you were mentioned.Message ID: @.***>