I wish to study helix to coil transformation in a protein when its unbound and when it interacts with other proteins. For molecular dynamics what would be an effect parameter choice for such study. Currently i am considering an implicit solvent MD approach however, would mesoscopic/reduced model or Go-like model or any other approach be more preferred?
Naga Srinivas Tripuraneni
Hi Manan,
You can try to consider RMSF changes during the transormations. Instead of implicit solvent model, try using TIP3P / TIP4P solvent models with appropriate salt and ion concentrations to get a better conclusion.
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