Hi,<div><br></div><div>Thanks a lot for the quick reply. I want to position restrain the head group atoms of CG DSPC but I am not sure about the head group molecules in DSPC. Can you please tell me how to figure out the head group atoms or molecules. Also, when you say co-ordinate file then you mean .itp file for the lipid right?</div>
<div><br></div><div>Thanks</div><div><br><div class="gmail_quote">On Wed, Jun 23, 2010 at 2:47 PM, 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>
sunny mishra wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All,<br>
<br>
I am trying to run the Position Restrained simulation for the Coarse Grained DSPC bi-layer. However, I am quite confused that how to generate the position restraint file for the CG atoms in lipid. Is there a difference between the position restraint file for the fine grained and coarse grained structures. Please let me know how to generate the position restraint file for Coarse Grained DSPC bi-layer. Your reply for the same will be highly appreciable.<br>
</blockquote>
<br></div>
You can generate a position restraint file for any molecule using genrestr. Just make sure to supply it with a coordinate file for a single molecule (i.e., not your entire bilayer), since position restraints are applied to moleculetypes, and not global structures.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thanks,<br>
<br>
Sunny<br>
<br>
</blockquote>
<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> | (540) 231-9080<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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