<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">try - cluster, and then as cluster group protein.<DIV>Kay.</DIV><DIV><BR><DIV><DIV>On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <DIV><FONT size="2">hi, all user:</FONT></DIV> <DIV> </DIV> <DIV><FONT size="2">i performed the dimer simulation, and want to realize the interaction between two peptides.</FONT></DIV> <DIV><FONT size="2">but frequently, i </FONT> <FONT size="2">encountered this kind of problem: sometimes peptides moved out of the box, and sometimes they jumped back.</FONT></DIV> <DIV><FONT size="2">i have tried so many way to pull them back with trjconv command, but still cause some unexpected problem.</FONT></DIV> <DIV><FONT size="2">for example, peptides break to many parts ( with -pbc whole ) or diffuse out of box gradually ( with -pbc nojump )</FONT></DIV> <DIV><FONT size="2">with -ur or -center still not the trajectory i really want. i think maybe there are some tricks to perform.</FONT></DIV> <DIV><FONT size="2">any suggestions for me ? thanks sooooooooooo much!</FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>