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julie-forman-kay-lab / IDPConformerGenerator

Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space
https://idpconformergenerator.readthedocs.io/
Apache License 2.0
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Explore the use of energy minimization on generated conformers #125

Open SeanR22 opened 3 years ago

SeanR22 commented 3 years ago

Energy minimization should clean-up many of the high energy structures generated with the build command. Build in a separate energy minimization module or add a flag to build command?

joaomcteixeira commented 3 years ago

Hi Sean,

Here in the group we have had this discussion multiple times. My opinion is that conformer minimization by MD simulation is an "advanced" topic where users will have the most various tastes on how to do such minimization. Therefore, I think implementing a module for that is not a good decision. Likely the module would also be a bridge to run a third-party package. Advanced users, like you, can perform the minimization with their preferred MD package.

However, example scripts of how to do such minimization with different MD packages are very welcomed.