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

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,



I have similar questions/doubts regarding this topic. I am trying to apply the following tutorial 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?