<div dir="ltr">But the problem is: how to define a boundary?<br><br>
<div class="gmail_quote">2008/10/10 Xavier Periole <span dir="ltr"><<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>></span><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">On Fri, 10 Oct 2008 15:09:31 +0800<br> "Lee Soin" <<a href="mailto:nomadoro@gmail.com" target="_blank">nomadoro@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi! I'm going to simulate a protein confined in a box. Can GROMACS do this?<br>Will the removal of the periodic boundary condition be OK?<br>
</blockquote></div>The removal of the periodic boundary conditions will be equivalent to an<br>infinite box. Unless you define the boundaries of your box (e.g. walls)<br>the protein (in solvent?) would not stop diffusing. This no problem but<br>
is this what you like?
<div class="Ih2E3d"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>-- <br>Sun Li<br>Department of Physics<br>Nanjing University, China<br></blockquote><br></div>-----------------------------------------------------<br>
XAvier Periole - PhD<br><br>- Molecular Dynamics Group -<br>NMR and Computation<br>University of Groningen<br>The Netherlands<br>-----------------------------------------------------<br>_______________________________________________<br>
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