Peggy,<br><br>You really have to do some background reading on molecular dynamics simulations... <br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div> After I ran an energy minimization, the CA2+ ended up outside of the box. Now I am really perplexed. What could be causing this behavior? </div></blockquote><div><br>See <a href="http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions">
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions</a><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Could anyone give me some advice? I'm at my wit's end.
</div></blockquote><div><br>Start with normal MD simulations, without bothering about calcium. <br>Later on, take your protein and put the calcium in by hand in the place(s) it should be. You can infer the coordinates from those of the coordinating oxygens.
<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>The water in the water box looks like ice cubes in an ice cube tray, segregated into regular little mini-boxes. I presume the latter is a numerical consequence of the CA2+ flying out of the box.
</div></blockquote><div><br>Very wrong. It's a consequence of building up a water box from smaller water boxes.<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<div>Many thanks for any help..</div>
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<div>Peggy</div>
<div> </div></blockquote></div><br>Cheers,<br><br>Tsjerk<br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands
<br>P: +31-30-2539931 <br>F: +31-30-2537623