So please look at the attached figure which is exactly the leftmost subfigure of Figure 4.8 from manual. Given one plane defined by (j,k,l), the cases where <case1> i is above the plane and <case2> below the plane can give the same dihedral angles. But chirality can distinguish the two cases: define chirality = ( (lk) x (kj) ) . (ji), then chirality is positive for <case1> and negative for <case2>. Am I right?<br>
<br><br><br><br><div class="gmail_quote">On Mon, Jan 30, 2012 at 6:01 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 31/01/2012 11:53 AM, Li SUN wrote:
<blockquote type="cite">Hello,<br>
<br>
I am doing pulling simulations with GROMACS and would like to keep
the chirality of the protein along the trajectory otherwise the
protein will take the wrong chirality especially at long
extensions. I have checked that using the improper dihedral or
dihedral restraint can restrain the dihedral, but dihedral
restraint is not equivalent to chirality restraint.</blockquote>
<br></div>
Why not? See 4.2.11 of manual and figure 4.8.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="im"><br>
<br>
<blockquote type="cite"> So I am wondering if there is a "chirality restraint"
somewhere in GROMACS. Otherwise I might have to modify the code...<br>
<br>
Thanks in advance!<br>
<br clear="all">
<br>
-- <br>
Li Sun<br>
Department of Physics<br>
University of California, San Diego<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div>
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