<div dir="ltr">I'm going to put two peptide chains in a box and study dimerization. I think confining them in a box can reduce conformational search.<br><br>
<div class="gmail_quote">2008/10/14 Jochen Hub <span dir="ltr"><<a href="mailto:jhub@gwdg.de">jhub@gwdg.de</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">Lee Soin wrote:<br>> Hello, all! I intend to simulate a protein confined in a box. Can anybody<br>> tell me how to define a boundary, or a wall, in GROMACS? Thanks!<br><br></div>As far as I know Berk has implemented walls in gromacs 4.0. Check the<br>
new mdp options. Are you sure that you do not want to use peridic<br>boundary conditions?<br><br>Best, Jochen<br><br>><br>><br>><br>> ------------------------------------------------------------------------<br>
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> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>************************************************<br>Dr. Jochen Hub<br>
Max Planck Institute for Biophysical Chemistry<br>Computational biomolecular dynamics group<br>Am Fassberg 11<br>D-37077 Goettingen, Germany<br>Email: jhub[at]<a href="http://gwdg.de/" target="_blank">gwdg.de</a><br>Tel.: +49 (0)551 201-2312<br>
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Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Sun Li<br>Department of Physics<br>
Nanjing University, China<br></div>