<span class="gmail_quote"><br></span>When I run simulations on a 42 residue peptide with a box size of 2.2 nm , I find that after 4 ns , the peptide comes out of the box . Is this a problem as far as the accuracy of the simulation results are concerned. Do the periodic conditions account for such cases? If not , is there any suggestion as to how I may salvage my data without having to start all over again .
<br><br>Cheers<br><br>Rakesh<br><br>Bachelors Student<br>Anna University<br>India<br>