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><span class="gmail_quote">On 5/10/06, <b class="gmail_sendername">Marcelo Fabricio Masman</b> <<a href="mailto:mmasman@gmail.com">mmasman@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<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><div style="direction: ltr;"><span class="sg">
<div> </div>
<div>Marcelo</div>
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</a><br><br></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
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