It performs an energy minimization on the generated model using user specified number of steps of steepest descent and conjugate gradient. For exhaustive minimization you can also use Gromacs.
Thank you so much for your response. This makes sense now. I wanted to know its function and I wanted to perform energy minimization using EasyModeller just as I have seen in Modeller. Thank you again.
Can you suggest me any other tool other than Gromacs? Any other online tool?
Furthermore, could you kindly tell me about the loop model button? It tells me to select a particular range of residues for my protein model. Are those residues based on the disordered regions of the proteins? I can predict the disordered regions and then select the residues for my loop model right? But I don't know which one to select for further evaluation as it provides me with two models after loop modeling. I've attached an image here. The first two models, I believe one of them is the refined loop model. If you could kindly differentiate between them, then it would be great.