@ Justin, That doesn’t sound very good. I tried it as he suggested using make_ndx, it seems to work, but it’s not reporting the result I want. When I use g_angle using the index i created, I chose the group I want to assess (My compound is very simple in Martini, it’s only represented by 3 atoms) and it reports back to me 1 angle value. However, I wish to assess the angle between atom 1 & 2, 2&3 and 1&3. How should I go about achieving that?
Thanks, Xu Huang On Oct 31, 2013, at 4:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/31/13 3:59 PM, Riccardo Concu wrote: >> Dear Xu, >> you have to use the make_ndx option if I'm not wrong. >> The syntax should be make_ndx -f xxx.gro -o index.ndx > > make_ndx is not particularly useful for angles. To get it to recapitulate > the function of mk_angndx, it's as much work as writing the index file by > hand. > > -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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > 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 -- 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
