# \#density-fit

**URL:** https://gromacs.bioexcel.eu/tag/density-fit/74.md

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## [Unexplained calculation stalling during density fit](https://gromacs.bioexcel.eu/t/unexplained-calculation-stalling-during-density-fit/12449)

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**Author:** [@YannLefrancois](https://gromacs.bioexcel.eu/u/YannLefrancois)\
**Replies:** 2\
**Last updated:** [August 25, 2025, 1:03pm UTC](https://gromacs.bioexcel.eu/t/unexplained-calculation-stalling-during-density-fit/12449 "2025-08-25T13:03:48Z")

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GROMACS version: 2024.4=mpi\_openmpi\_cuda\_he6b8466\_0 (conda distribution) GROMACS modification: Yes/No I’m trying to do density fitting, following the bioexcel webinar #82, when i look at my performance log I see this …

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## [Density is reducing after nvt equilibration follwed by md production](https://gromacs.bioexcel.eu/t/density-is-reducing-after-nvt-equilibration-follwed-by-md-production/12540)

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**Author:** [@sanket\_singare](https://gromacs.bioexcel.eu/u/sanket_singare)\
**Replies:** 0\
**Last updated:** [August 19, 2025, 10:25am UTC](https://gromacs.bioexcel.eu/t/density-is-reducing-after-nvt-equilibration-follwed-by-md-production/12540 "2025-08-19T10:25:39Z")

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GROMACS version: GROMACS modification: Yes/No Here post your question Hello Users, I am doing md simulation in which for npt production i am getting actual density of solvent , but after doing nvt equilibration, foll…

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## [Density mediated simulation fine refinement](https://gromacs.bioexcel.eu/t/density-mediated-simulation-fine-refinement/5901)

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**Author:** [@dave](https://gromacs.bioexcel.eu/u/dave)\
**Replies:** 1\
**Last updated:** [March 3, 2023, 7:15am UTC](https://gromacs.bioexcel.eu/t/density-mediated-simulation-fine-refinement/5901 "2023-03-03T07:15:57Z")

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GROMACS version: gromacs-2022.2 GROMACS modification: No Hi All, (maybe more relevant to Dr. Christian Blau) It has been long I did not do MD simulations. I came across an old Bioexcel webinar about density mediated …

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## [Density guided simulation setup](https://gromacs.bioexcel.eu/t/density-guided-simulation-setup/5108)

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**Author:** [@owen](https://gromacs.bioexcel.eu/u/owen)\
**Replies:** 5\
**Last updated:** [November 2, 2022, 9:51am UTC](https://gromacs.bioexcel.eu/t/density-guided-simulation-setup/5108 "2022-11-02T09:51:57Z")

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GROMACS version: 2022.3 GROMACS modification: No Running density guided simulations are very slow due to it switching off domain decomposition (guessing from the log message). The simulations are running at \<10ns per d…

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## [Density map guided MD: pbc and protein fitting to the density map](https://gromacs.bioexcel.eu/t/density-map-guided-md-pbc-and-protein-fitting-to-the-density-map/236)

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**Author:** [@fabrizio](https://gromacs.bioexcel.eu/u/fabrizio)\
**Replies:** 1\
**Last updated:** [September 28, 2020, 1:03pm UTC](https://gromacs.bioexcel.eu/t/density-map-guided-md-pbc-and-protein-fitting-to-the-density-map/236 "2020-09-28T13:03:09Z")

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GROMACS version: 2020.2 Hi all, I have the structure of a protein and the cryoEM density map used to generate the structure. I want to use the density map to refine the structure through MD using the GROMACS 2020 densi…