Thanks for the explanation! Is the improper dihedral in GROMACS implemented in an unsigned fashion?<div><br></div><div><br><div><br><div class="gmail_quote">On Mon, Jan 30, 2012 at 9:01 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 31/01/2012 2:59 PM, Li SUN wrote:
<blockquote type="cite">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.</blockquote>
<br></div>
Only if they are measured in a unsigned fashion.<div class="im"><br>
<br>
<blockquote type="cite"> 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>
</blockquote>
<br></div>
During the flipping process, the energy/force from the dihedral
restraint potential will increase because the angle deviates from
the programmed one. This will act to prevent flipping occurring
without needing to trouble with computing a signed dihedral angle.
If you pull too hard, then the restraint has insufficient effect.
Choose wisely.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="im"><br>
<br>
<blockquote type="cite">
<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" target="_blank">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> 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><font color="#888888"><br>
<br>
Mark</font></span>
<div><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>
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<br>
</blockquote>
<br>
</div>
</div>
<br>
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</div>
<br>
<br clear="all">
<br>
-- <br>
Li Sun<br>
Department of Physics<br>
University of California, San Diego<br>
<br>
<fieldset></fieldset>
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</blockquote>
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University of California, San Diego<br>
</div></div>