On 31/01/2012 2:59 PM, Li SUN wrote:
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.
Only if they are measured in a unsigned fashion.
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?
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.
Mark
On Mon, Jan 30, 2012 at 6:01 PM, Mark Abraham <mark.abra...@anu.edu.au <mailto: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. MarkSo I am wondering if there is a "chirality restraint" somewhere in GROMACS. Otherwise I might have to modify the code... Thanks in advance!-- Li SunDepartment of Physics University of California, San Diego-- gmx-users mailing list gmx-users@gromacs.org <mailto: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 <mailto: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
-- 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
