# Density map guided MD: pbc and protein fitting to the density map

**URL:** <https://gromacs.bioexcel.eu/t/density-map-guided-md-pbc-and-protein-fitting-to-the-density-map/236>\
**Category:** User discussions\
**Tags:** density-fit\
**Created:** [June 3, 2020, 11:20am UTC](https://gromacs.bioexcel.eu/t/density-map-guided-md-pbc-and-protein-fitting-to-the-density-map/236 "2020-06-03T11:20:57Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![fabrizio](https://avatars.discourse-cdn.com/v4/letter/f/8dc957/32.png) [@fabrizio](https://gromacs.bioexcel.eu/u/fabrizio)\
**Post date:** [June 3, 2020, 11:20am UTC](https://gromacs.bioexcel.eu/t/density-map-guided-md-pbc-and-protein-fitting-to-the-density-map/236/1 "2020-06-03T11:20:57Z")

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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 density-guided simulation tool. My doubts:

- how to treat the pbc with density guided MD and how the size of the boxes should be? How to visualize the size of the density map box?

- fitting the protein structure to the density map: any suggestion on how to do it? So far I tried with Chimera without obtaining good results.

Thanks for your help,

Fabrizio

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**Author:** ![georg](https://avatars.discourse-cdn.com/v4/letter/g/9f8e36/32.png) [@georg](https://gromacs.bioexcel.eu/u/georg)\
**Post date:** [September 28, 2020, 1:03pm UTC](https://gromacs.bioexcel.eu/t/density-map-guided-md-pbc-and-protein-fitting-to-the-density-map/236/2 "2020-09-28T13:03:09Z")

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Hi,

I have similar questions/doubts regarding this topic. I am trying to apply the following tutorial [https://github.com/moozzz/simulation-protocols/tree/master/cdmd-aldolase-refinement](https://github.com/moozzz/simulation-protocols/tree/master/cdmd-aldolase-refinement) to a different structure. As suggested in the tutorial, I ran `gmx editconf -f gmx_structure.pdb -o gmx_structure_box.pdb -bt triclinic -d 1.0 -center x_c y_c z_c` (with x\_c etc. substituted by center of mass coordinates) to make the box larger and not shift the molecule in respect to the density map. When I checked the files after solvation, the solvent molecules were added around symmetry-related coordinates (but still following pbc I guess). After minimization/equilibration also the protein coordinates were shifted to the symmetry mate in the .gro file which serves as input for the density-guided MD.

Can this shift be a problem for density alignment or is the density also treated in a periodic manner?

Is there a way to avoid this coordinate shift to a symmetry mate in the first place?

Thanks,  
Georg