# \#biobb

**URL:** https://ask.bioexcel.eu/tag/biobb/2.md

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## [Threshold value](https://ask.bioexcel.eu/t/threshold-value/6042)

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**Author:** [@itsPriyanka](https://ask.bioexcel.eu/u/itsPriyanka)\
**Replies:** 3\
**Last updated:** [March 19, 2026, 11:27am UTC](https://ask.bioexcel.eu/t/threshold-value/6042 "2026-03-19T11:27:10Z")

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I have done the HADDOCK docking. I am getting the results for Cluster 1. HADDOCK score -100.5 +/- 2.7 Cluster size 62 RMSD from the overall lowest-energy structure 1.…

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## [NVT vs NPT for Non-Equilibrium Switching in pmx/GROMACS](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980)

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**Author:** [@EidRashed](https://ask.bioexcel.eu/u/EidRashed)\
**Replies:** 1\
**Last updated:** [January 26, 2026, 11:19am UTC](https://ask.bioexcel.eu/t/nvt-vs-npt-for-non-equilibrium-switching-in-pmx-gromacs/5980 "2026-01-26T11:19:35Z")

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I’m using pmx + GROMACS to run non-equilibrium alchemical free energy calculations for large protein–protein interactions (e.g., ~150 k atoms, like Fc–FcRn). My workflow is essentially: Equilibrate both end states (st…

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## [Protein-protein docking parameters](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776)

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**Author:** [@Negin](https://ask.bioexcel.eu/u/Negin)\
**Replies:** 2\
**Last updated:** [July 1, 2025, 9:48am UTC](https://ask.bioexcel.eu/t/protein-protein-docking-parameters/5776 "2025-07-01T09:48:29Z")

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Hello I would like to perform protein-protein docking, and I do not have any experimental data showing how they are interacting and what is the binding interface of them. But, I used PesTo webserver and other online too…

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## [Example for software feedback](https://ask.bioexcel.eu/t/example-for-software-feedback/5176)

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**Author:** [@alevil](https://ask.bioexcel.eu/u/alevil)\
**Replies:** 0\
**Last updated:** [July 5, 2024, 1:18pm UTC](https://ask.bioexcel.eu/t/example-for-software-feedback/5176 "2024-07-05T13:18:25Z")

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Topic: Feedback on GROMACS, HADDOCK, BioBB and PMX Feedback: write the features you would like to be implemented in the future and ideas to improve the core applications. Login to post, select the sub-category softwar…