I do not see that the caption to figure 4.8 implies a "reference" atom. It talks merely about the angle between planes i-j-k and j-k-l. That angle is signed and the sign is significant for equation 4.60. Does the sign of the angle differ from that between l-k-j and k-j-i? I think not, but it's way too late here for me to wrap my right-hand-rule for cross-products around that one! :-)
Mark On Tue, Apr 30, 2013 at 2:06 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/29/13 8:00 PM, Mark Abraham wrote: > >> 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.) >> >> > I have always interpreted Figure 4.8 to imply that if one changes the > order of the atoms (ai, aj, ak, al in the topology), the planes defined > around the reference atom would be different for a given set of 4 atoms in > different order. Is this not the case? I haven't gone into the code to > see how the topology is interpreted. > > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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