<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Zhen Chen<br><br>Protein is located stranger(sometime at the one side of the protein,in other frame other side). Its not a problem. Your simulation is fine. it is due to you had given PBC. thats why. You can reset your trejectory using trjconv.<br><br><br>regards<br><div><br><span style="color: rgb(56, 83, 118); font-family: comic sans ms;">Ravi Datta Sharma</span></div> <div><span style="color: rgb(56, 83, 118); font-family: comic sans ms;">Lecturer,</span></div> <div><span style="color: rgb(56, 83, 118); font-family: comic sans ms;">Bioinformatics,</span><br style="color: rgb(56, 83, 118); font-family: comic sans ms;"><span style="color: rgb(56, 83, 118); font-family: comic sans ms;">Department of Microbiology,<br>CCS Unversity,<br>Meerut</span><span style="color: rgb(56, 83, 118); font-family: comic sans
ms;"><br> <br></span></div><br><br>--- On <b>Wed, 3/6/09, sheerychen <i><sheerychen@gmail.com></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: sheerychen <sheerychen@gmail.com><br>Subject: [gmx-users] protein running out of box<br>To: gmx-users@gromacs.org<br>Date: Wednesday, 3 June, 2009, 7:07 PM<br><br><div id="yiv12970295">Hello, every body. I have running a MD for 10ns. However, after 5ns part of protein will running out of the box and be located at other part of the water box. And the whole structure seems ver strange. It
seems that it was caused by the mass translation but I have used the comm_mode=Linear. Any suggestions?<br clear="all">
<br>-- <br>Zhen Chen,<br>Department of Bioprocess and Biosystem Engineering,<br>Hamburg University of Technology, Denickestr. 15, D-21071, Hamburg,Germany<br>Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: <a rel="nofollow" ymailto="mailto:zhen.chen@tuhh.de" target="_blank" href="/mc/compose?to=zhen.chen@tuhh.de">zhen.chen@tuhh.de</a><br>
</div><br>-----Inline Attachment Follows-----<br><br><div class="plainMail">_______________________________________________<br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="/mc/compose?to=gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></div></blockquote></td></tr></table><br>
<!--1--><hr size=1></hr> Bollywood news, movie reviews, film trailers and more! <a href="http://in.rd.yahoo.com/tagline_movies_1/*http://in.movies.yahoo.com/?wm=n/"> Click here.</a>