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.abra...@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 > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Li Sun Department of Physics University of California, San Diego
<<attachment: chi.png>>
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