<div>Eugenia,</div>
<div> </div>
<div>this is only a visualization issue. Try the options -pbc nojump/whole/inbox in trjconv.</div>
<div><br>Regarding comm_mode, I think you should use linear.</div>
<div> </div>
<div>Regards,</div>
<div> </div>
<div>Pedro.<br> </div>
<div><span class="gmail_quote">2007/1/30, Eugenia Polverini <<a href="mailto:eugenia.polverini@fis.unipr.it">eugenia.polverini@fis.unipr.it</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear all,<br>in the output of my 5 ns MD of a small protein in a box of water and<br>pbc, I see that during MD the protein goes out from the box.
<br>Why it happened? Is it a problem or I can accept that all was OK?<br>I have set the comm_mode=angular.<br><br>Thanks for your help!<br>Best regards<br>Eugenia<br><br><br><br>--<br>Eugenia Polverini, Ph.D.<br>Dept. of Physics
<br>University of Parma<br>Parco Area delle Scienze, 7/A<br>43100 Parma<br>ITALY<br><br>Phone: +39 0521 905254<br>Fax: +39 0521 905223<br>E-Mail: <a href="mailto:eugenia.polverini@fis.unipr.it">eugenia.polverini@fis.unipr.it
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