Re: [gmx-users] Dihedral potential with chirality

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 wrote: > On 31/01/2012 2:59 PM, Li SUN wrote: > > So please look at the attached figure which is exactly the leftmost > subfigure o

Re: [gmx-users] Dihedral potential with chirality

= ( (lk) x (kj) ) . (ji), then chirality is positive for and negative for . Am I right? On Mon, Jan 30, 2012 at 6:01 PM, Mark Abraham 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 > chiral

[gmx-users] Dihedral potential with chirality

dihedral, but dihedral restraint is not equivalent to chirality restraint. 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 --