<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks. That solves the problem. But I still see this warning message: <div><br></div><div><div>Steepest Descents did not converge to Fmax < 10 in 201 steps.</div><div>Potential Energy = -1.2866480e+05</div><div>Maximum force = 3.4851584e+03 on atom 3683</div><div>Norm of force = 6.3128883e+01</div><div><br></div><div>That means I should run longer energy minimization until it converges well and I don't see this error message. Is that right?</div><div>Thanks.</div><div><br></div><div>Zhong</div></div><div><br><div><div>On May 12, 2009, at 12:46 AM, Pawan Kumar wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">hi,<br><br>Defining a specific box size with -d option in editconf will help to overcome this problem...<br><br>Regards,<br>Pawan <br><br><div class="gmail_quote">On Tue, May 12, 2009 at 8:05 AM, Zhong Zheng <span dir="ltr"><<a href="mailto:zhozheng@gmail.com">zhozheng@gmail.com</a>></span> wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">hi all<br> <br> I am running Gromacs on a protein consisted of three chains. But no matter how I tried, the protein always falls into three parts (corresponding to each chain) after a simple 2000 steps energy minimization. Can anyone help me please? Thanks.<br> <font color="#888888"> <br> Zhong Zheng<br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">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 thewww interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">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><br> </font></blockquote></div><br> _______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></body></html>