Thanks for the explanation! Is the improper dihedral in GROMACS implemented in an unsigned fashion?
On Mon, Jan 30, 2012 at 9:01 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > 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>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 > > > > > -- > 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
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