<div dir="ltr"><div class="gmail_extra">Thanks dear Justin.</div><div class="gmail_extra"> </div><div class="gmail_extra">No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run.</div>
<div class="gmail_extra">I could see the Pos. Res. works in md.log file.</div><div class="gmail_extra"> </div><div class="gmail_extra">Regards,</div><div class="gmail_extra">Dariush<br><br></div><div class="gmail_quote">On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote"><div class="HOEnZb"><div class="h5"><br>
<br>
On 4/26/12 1:35 PM, Dariush Mohammadyani wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
Dear All,<br>
I am using CG-MD using MARTINI forcefield. The system contains Protein and lipid<br>
bilayer. Although I used:<br>
define = -DPOSRES<br>
components in system were moving around and interact with each other. Then, I<br>
cannot do NVT or NPT equilibration.<br>
Could you please let me know how can I control this kind of movements?<br>
</blockquote>
<br></div></div>
If molecules that should be restrained are moving inappropriately, then the restraints are not being replied properly in the topology. In the absence of more substantial information, there's nothing else that can be said.<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" target="_blank" value="+15402319080">(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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