[gmx-users] Dihedral potential with chirality

Li SUN nomadoro at gmail.com
Tue Jan 31 04:59:40 CET 2012

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?

On Mon, Jan 30, 2012 at 6:01 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 31/01/2012 11:53 AM, Li SUN wrote:
> Hello,
> 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.
> Why not? See 4.2.11 of manual and figure 4.8.
> Mark
>  So I am wondering if there is a "chirality restraint" somewhere in
> GROMACS. Otherwise I might have to modify the code...
> Thanks in advance!
> --
> Li Sun
> Department of Physics
> University of California, San Diego
> --
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Li Sun
Department of Physics
University of California, San Diego
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