<font color="#000099"><font face="verdana,sans-serif">How's position restraint? If the force constant is reduced (reduce the number in posre.itp ?), the simulation will lead to more flexible structure?<br></font></font><br>
<div class="gmail_quote">On Mon, Oct 10, 2011 at 10:20 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 class="im"><br>
<br>
Liu, Liang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks.<br>
<br>
Will the constrain help?<br>
<br>
</blockquote>
<br></div>
Bond constraints? Well, in general, they're useful, and likely necessary at high temperature to keep your system stable. Please be more specific.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Liu, Liang wrote:<br>
<br>
Hi, all,<br>
<br>
I am trying to use Gromacs to obtain structural ensembles around<br>
native structures (PDB structures).<br>
However the simulated structures are always very close to the<br>
initial one, with RMSD < 0.2.<br>
I am wondering how to obtain large-RMSD structures? Thanks.<br>
<br>
<br>
Large RMSD values would indicate non-native structures, which<br>
doesn't sound like what you're looking for. If your goal is simply<br>
enhanced sampling, try REMD.<br>
<br>
-Justin<br>
<br></div>
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ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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Best,<br>
Liang Liu<br>
</div></blockquote><div><div></div><div class="h5">
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-- <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>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>