The manual does discuss restraining to a plane, but this must be the plane in which the atom is already present.<div><br></div><div>[ position_restraints ]</div><div>; ai funct fc</div><div>...</div><div>3 1 1000 0 0 </div>
<div><br></div><div>How about restraining the atom to some other plane? For example, how about restraining a phosphate group initially at the lipid-water interface to the bilayer center (for whatever fancy reasons) ? Won't this require pulling the atom to that plane first?</div>
<div><br></div><div>If it can be achieved using the position restraints alone, it is not clear to me how to do this? </div><div><br></div><div>-Maria<br><div><br></div><div><br><br><div class="gmail_quote">On Tue, Sep 7, 2010 at 12:53 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>
maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I want to restrain certain atoms of my simulation to the plane perpendicular to the bilayer normal, and at the bilayer center. Can someone please provide a quick guide on how to do this? I read the pull-code options, but restraining to a plane did not seem possible?<br>
<br>
</blockquote>
<br></div>
You can restrain atoms to a plane using position restraints. See the manual for an example.<br><font color="#888888">
<br>
-Justin</font><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<br>
</blockquote>
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-- <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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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br>
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