On Mon, Apr 29, 2013 at 11:34 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > Please start a new thread if you're going to introduce a new topic. I > have changed the subject to something more relevant. > > On 4/29/13 4:23 PM, lloyd riggs wrote: > >> *Dear All,* >> *Doing a water/temp energy minimization just for a figure with a large >> molecule >> that has several connected parts, I ran into a bizzar question.* >> *So I found its possible by accident to define improper dihedrails >> forwards and >> backwards without gromacs complaining, such as atom 1 2 3 4 and 4 3 2 1. >> My >> question is, if your topology has this, does it affect the calculations >> (angle >> energy or other)?* >> > > Yes, it does. For impropers, the order matters. In the two examples, you > are specifying different properties. With "1 2 3 4," you are saying that > atom 1 is planar and atoms 2, 3, and 4 are the atoms around it that govern > its planarity. With "4 3 2 1," you are saying atom 4 is the planar center, > with atoms 1, 2, and 3 similarly governing its planarity. > I didn't know that. A quick look in the manual didn't reveal where we have that documented. Do we? (Obviously, it is only applicable to harmonic-type improper dihedrals.) Mark -- 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
