% Density guided simulations
% Christian Blau
% 2019-12-09 - Janssen

# Treating cryo-EM data

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# Fitting structures to densities

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## Simulation setup requirements

- "vanilla" GROMACS simulation
- add density in .mdp options
- apply forces that increase similarity with density

## Exploring structural ensembles

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## Choice of force-constant

- determine balance between influence from force-field and from map

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# GLIC - avoiding model building

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# Connecting structure and density

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- EM densities report the number of electron-atom interactions per Volume

## Assumptions {#nobg}


- Interaction is defined by interaction cross-section and motion of atoms

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# Summary

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