<font color="#000099"><font face="verdana,sans-serif">Well, I am only trying to get structures with some of them far from the initial structure (large RMSD) and some of them close to the initial one...<br></font></font><br>
<div class="gmail_quote">On Mon, Oct 10, 2011 at 10:37 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Liang Liu,<br>
<br>
You will never get broader sampling by adding restraints. If you want<br>
to have broader sampling, raise the temperature or add denaturants.<br>
But also ask yourself the question if what you think you want is what<br>
you should be wanting. What is the actual question you're trying to<br>
solve?<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="h5"><br>
On Mon, Oct 10, 2011 at 5:32 PM, Liu, Liang <<a href="mailto:liu4gre@gmail.com">liu4gre@gmail.com</a>> wrote:<br>
> How's position restraint? If the force constant is reduced (reduce the<br>
> number in posre.itp ?), the simulation will lead to more flexible structure?<br>
><br>
> On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
>><br>
>><br>
>> Liu, Liang wrote:<br>
>>><br>
>>> Thanks.<br>
>>><br>
>>> Will the constrain help?<br>
>>><br>
>><br>
>> Bond constraints? Well, in general, they're useful, and likely necessary<br>
>> at high temperature to keep your system stable. Please be more specific.<br>
>><br>
>> -Justin<br>
>><br>
>>> On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a><br>
>>> <mailto:<a href="mailto:jalemkul@vt.edu">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>
>>> -- ==============================__==========<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="http://vt.edu" target="_blank">http://vt.edu</a>> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
>>> <tel:%28540%29%20231-9080><br>
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>>> <<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>><br>
>>><br>
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>>><br>
>>><br>
>>><br>
>>><br>
>>> --<br>
>>> Best,<br>
>>> Liang Liu<br>
>><br>
>> --<br>
>> ========================================<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">(540) 231-9080</a><br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>><br>
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><br>
><br>
><br>
> --<br>
> Best,<br>
> Liang Liu<br>
><br>
> --<br>
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<br>
<br>
<br>
--<br>
</div></div><div class="im">Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>