<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi all,</span></div><div><br><span></span></div><div><span>I simulated a protein in water. When I get its 20 ns trajectory and load it in VMD, I see some bonds stretch suddenly and moves far strangely! Is this problem because of the wrong structure of the protein? Or I may put some restrains on system and solve this problem?</span></div><div><span>Anybody may suggest me in this about?<br></span></div><div><br><span></span></div><div><span>Thank you.<br></span></div><div> </div><div>Sincerely,<br>Shima</div></div></body></html>