<font color="#000099"><font face="verdana,sans-serif">Thanks.</font></font><div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">Will the constrain help?<br>
</font></font><br><div class="gmail_quote">On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
<br>
Liu, Liang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi, all,<br>
<br>
I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures).<br>
However the simulated structures are always very close to the initial one, with RMSD < 0.2.<br>
I am wondering how to obtain large-RMSD structures? Thanks.<br>
<br>
</blockquote>
<br></div></div>
Large RMSD values would indicate non-native structures, which doesn't sound like what you're looking for. If your goal is simply enhanced sampling, try REMD.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>
</div>