Thanks Justin for the quick reply. I am simulating a protein with bound lipids. I am in a dilemma to choose the direction of the normal to calculate order parameter. In your *Membrane-protein *simulation tutorial, you have chosen normal to the bilayer along the z-axis. But in my case, there is no bilayer, infact, only few bound lipids are there. In which direction I should choose the normal (*-d option*)?
On Thu, Aug 1, 2013 at 10:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/1/13 12:07 PM, Venkat Reddy wrote: > >> Dear Gmx-users, >> In the GROMACS site, it has been mentioned that there is a bug (Instead of >> numbering carbons from 2-17, the numbering starts from 1-16) in g_order >> program up to, and including, v4.5.4. But when I am using v4.5.5, I am >> getting the same sort of numbering. Is it normal or I should renumber from >> 2-17? >> >> > If you're getting a number starting with 1, it's probably wrong. You > can't calculated Scd for the first carbon in a chain because there is no > n-1 carbon from which to determine the necessary vectors. Someone > (probably me) updated the wiki when version 4.5.4 was current, so probably > any 4.5.x version is really affected, and 4.6.x may be as well, since this > really is just a trivial bug that requires simple reinterpretation. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > 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> > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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
