<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">Dear All,<br><div id="yiv466925414"><div><div style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255); font-family: times new roman,new york,times,serif; font-size: 12pt;"><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></div></div><meta http-equiv="x-dns-prefetch-control" content="on"><br><br> </div> </div> </div></body></html>