<div dir="ltr">In short - you can apply PBC in all directions (XYZ) by choosing the proper keyword in the .mdp file, I believe the box dimensions are defined in .gro file.<br>Omer.<br clear="all"> <br>Koby Levy research group,<br>
Weizmann Institute of Science. <br><a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
<br><br><div class="gmail_quote">On Fri, Oct 10, 2008 at 16:00, Lee Soin <span dir="ltr"><<a href="mailto:nomadoro@gmail.com">nomadoro@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;">
<div dir="ltr">Maybe I didn't put it clearly. My intention is to simulate a protein confined in a box, and the problem is that I don't know how to define a boundary, or a wall, in GROMACS.<br></div></blockquote></div>
<br></div>