Search the manual about freezing groups. I think the command is freezegrps. This will fix the atoms in space.<br><br>--Venk<br><br><div class="gmail_quote">On Sun, Nov 22, 2009 at 7:25 AM, udi <span dir="ltr"><<a href="mailto:udi_zel@012.net.il">udi_zel@012.net.il</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 link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal">Hello all Gromacs users,</p>
<p class="MsoNormal">I’m simulating a 255 a.a peptide which is only a
segment of a whole protein.</p>
<p class="MsoNormal">I’m using the triclinic box with -d 1.2 nm.</p>
<p class="MsoNormal">Because the peptide is only a segment out of a larger
protein I would like to restrain the ends of the peptide in order to prevent
the peptide </p>
<p class="MsoNormal">from closing on its self during the simulation.</p>
<p class="MsoNormal">I thought to apply distance restraint in order to do so.</p>
<p class="MsoNormal">Using VMD I measured the distance between the C-alphas of
the first and last a.a. of the peptide and got 88.8A.</p>
<p class="MsoNormal">I wanted to double check the distance, so I used g_dist and
g_mindist and got a 56A!!! </p>
<p class="MsoNormal">I guess that PBC is the reason for the difference.</p>
<p class="MsoNormal">Which distance (VMD or Gromacs) should I use when applying
the distance restraint? </p>
<p class="MsoNormal">Is such a distance restrain (88.8A) even possible? (too
long?)</p>
<p class="MsoNormal">I would be glad to learn any other way to enforce a minimal
movement of the ends of the peptide.</p>
<p class="MsoNormal">Thanks in advance,</p>
<p class="MsoNormal">Udi</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> </p>
</div>
</div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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>__________________________________<br>
Venkatesh Hariharan<br>Columbia University | Biomedical Engineering<br>Graduate Research Assistant<br><br>"You must be the change you wish to see in the world."<br>--Mohandas Karamchand Gandhi<br><br>