<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt">Dear All,<br><br>I planned to use the method introduced in the Umbrella Sampling on-line tutorial of <font face="Arial"><b>Justin Lemkul </b></font>(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html). <br><br>But if a peptide is surrounded by a protein, which means the opening of the protein-complex is not large enough to allow the peptide to leave the protein without significantly breaking the conformation of the protein in the protein-peptide complex, is the Umbrella Sampling method still valid for the binding energy calculation?<br><br>Will you please also show me in which part of the tutorial the direction of pull-apart is defined? We should process it in a direction the peptide can leave the protein, not the direction protein will bind the peptide much strongly.<br><br>I am looking
forward to getting a reply from you.<br><br>Cheers,<br><br>Acoot<br></div></body></html>