# Out of memory issue while using MDweb GROMACS simulation

**URL:** <https://ask.bioexcel.eu/t/out-of-memory-issue-while-using-mdweb-gromacs-simulation/4731>\
**Category:** MDWeb\
**Created:** [December 16, 2023, 8:51am UTC](https://ask.bioexcel.eu/t/out-of-memory-issue-while-using-mdweb-gromacs-simulation/4731 "2023-12-16T08:51:30Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![SJLee](https://avatars.discourse-cdn.com/v4/letter/s/e95f7d/32.png) [@SJLee](https://ask.bioexcel.eu/u/SJLee)\
**Post date:** [December 16, 2023, 8:51am UTC](https://ask.bioexcel.eu/t/out-of-memory-issue-while-using-mdweb-gromacs-simulation/4731/1 "2023-12-16T08:51:30Z")

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Thank you for the amazing program  
Input pdb file was a receptor and a vaccine ligand complex of 1796 amino acids in total  
After full MD setup for GROMACS, I ran it with NPT option  
but it gives me an error as the one below

Type: MD\_TrajectoryXTC  
MD\_TrajectoryXTC…  
Out of memory!

Is it just due to the size of my input file?  
And is it proper to use NPT option to check the stability of such input?

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**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\
**Post date:** [December 18, 2023, 9:07am UTC](https://ask.bioexcel.eu/t/out-of-memory-issue-while-using-mdweb-gromacs-simulation/4731/2 "2023-12-18T09:07:21Z")

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Dear SJLee,

yes, it could well be a problem related to the size of your input file.

I would recommend you to take a look at our new tools, as MDWeb is a very old infrastructure running with obsolete MD packages. I would try it with:

- BioExcel Building Blocks library (and workflows):  
[Homepage - BioExcel Building Blocks](https://mmb.irbbarcelona.org/biobb/)  
[Workflows - BioExcel Building Blocks](https://mmb.irbbarcelona.org/biobb/workflows)

- MDWeb-like website using the previous library:  
[Homepage - BioExcel Building Blocks Workflows](https://mmb.irbbarcelona.org/biobb-wfs/)

Hope this helps!

Thanks for using our tools!

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**Author:** ![gcdomingo](https://avatars.discourse-cdn.com/v4/letter/g/a87d85/32.png) [@gcdomingo](https://ask.bioexcel.eu/u/gcdomingo)\
**Post date:** [January 3, 2024, 12:06pm UTC](https://ask.bioexcel.eu/t/out-of-memory-issue-while-using-mdweb-gromacs-simulation/4731/3 "2024-01-03T12:06:22Z")

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Hi! I try to use BioBB server but it won’t work, I cannot submit a project. It only says uploading data when i submit my protein-ligand structure it does not go to step 2:protonation state. can you help me with this?

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**Author:** ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\
**Post date:** [January 5, 2024, 10:19am UTC](https://ask.bioexcel.eu/t/out-of-memory-issue-while-using-mdweb-gromacs-simulation/4731/4 "2024-01-05T10:19:11Z")

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Dear gcdomingo,

we are experiencing technical problems with our computational resources behind the servers. We are working on fixing them. Please be patient and try it next week.

Thanks for your interest in our tools!