<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear gmx friends,</span></div><div><br><span></span></div><div><span>I put a protein in a simulation box filled of water molecules and entered the mdrun command. After the simulation, I found the protein near one of the edges of the box and not in center. What is the problem? Anyone may suggest me? <br></span></div><div><span>Does it mean that the simulation is meaningless? <br></span></div><div><span>I expect the protein to stay in the center of box and goes unfold by passing the time.<br></span></div><div> <br>Thanks in advance<br></div><div>Sincerely,<br>Shima</div></div></body></html>