Brief description of tools/files: charmm-GUI
How the work has been tested/reviewed:
Can one perform energy minimization with position restraints as given in the files generated by charmm-GUI? Is it the right way to do energy minimization?
What you are provided from CHARMM-GUI are the recommended protocols from the authors of whatever module you’re using. You’re free to depart from those inputs in whatever way(s) you see fit, but if things don’t work, it’s probably because the protocols are generally pretty robust and used for many years. See individual publications for whatever modules you’re using (Solution Builder, Membrane Builder, etc), which detail the protocol. The 2016 CHARMM-GUI paper talks about how we’ve validated the implementation across software for some general systems.
Thank you so much. I am preparing a system of membrane and protein using Charmm-GUI and I wanted to understand the reason behind putting the position restraints “-DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0” during the minimization step.
At various points during minimization and equilibration, some species are recommended to be restrained with different strengths, and some are sequentially switched off to fully relax the system. Again, this should be in Membrane Builder publications.
Thank you so much for your reply. I’ll go through their papers.