<div> </div>
<div>Thank you very much for your recommendations, Tsjerk.</div>
<div> </div>
<div>Marcelo<br><br> </div>
<div><span class="gmail_quote">On 5/10/06, <b class="gmail_sendername">Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div style="DIRECTION: ltr">Marcelo,<br><br>Have you considered reading the FAQ, searching the mailing list, reading the manual or just paying attention? Just yesterday there was mention of a ligand jumping out of the box, to which several replies were given and your exact question is asked on this list at least every month!
<br><br>I'll keep my temper. It's just due to the periodic boundary conditions, nothing wrong, you can use trjconv with option -pbc nojump afterwards or you can set comm_mode to linear with the protein as comm_group. Now please read the manual on periodic boundary conditions and for further reference search the mail list (
e.g. "periodic boundary conditions", "PBC", "jumping", etc...)<br><br>Tsjerk<br><br>
<div></div>
<div style="DIRECTION: ltr"><span class="e" id="q_10b1d78c59f993ee_1"><span class="gmail_quote">On 5/10/06, <b class="gmail_sendername">Marcelo Fabricio Masman</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:mmasman@gmail.com" target="_blank">
mmasman@gmail.com</a>> wrote:</span></span></div>
<div style="DIRECTION: ltr">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"></blockquote></div>
<div style="DIRECTION: ltr"><span class="e" id="q_10b1d78c59f993ee_3">
<div style="DIRECTION: ltr">
<div>Hello gmx users:</div>
<div> </div>
<div>I am running a very common MD simulation and the protein system is getting OUT of the box after approximately 200 ps. I have tried several things.</div>
<div>Does it happen very frequently? (common mistake)</div>
<div>Is there any way to keep, during the whole calculation, the protein system into the center of the box?</div>
<div>What could I do for avoiding this phenomenon?</div>
<div> </div>
<div>Thanks in advance.</div></div></span></div>
<div style="DIRECTION: ltr">
<div style="DIRECTION: ltr"><span>
<div> </div>
<div>Marcelo</div></span></div><br>_______________________________________________<br>gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">
gmx-users@gromacs.org</a><br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">
http://www.gromacs.org/mailing_lists/users.php </a><br><br>
<blockquote></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen
<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br> </div><br>_______________________________________________<br>gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">
http://www.gromacs.org/mailing_lists/users.php</a><br><br></blockquote></div><br>