Bad choice of words. Did not mean to suggests there's actual program bug. -Shay
-----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Wednesday, December 02, 2009 00:46 To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_mindist , trajectory only CA atoms, to small values? t.peter.muel...@gmx.net wrote: > Dear Shay, dear Gromacians > >> For purposes of debugging this bug you can also use the flag of g_mindist >> that gives out atom pairs and see which atom pairs is it that gromacs >> thinks are less the 1 angstrom. > I used the "-o atm-pair.out" option to get the atom pairs with the minimal > distance. For the all atom trajectory the correct atom pairs are selected. > But for the CA trajectory the wrong atom pairs are selected. Instead of the > pairs with the shortest distance a much further pair is selected. Although Can you post some of this output? > the output pair from "atm-pair.out" has a distance of more then 100 Angstrom > the value in the file "mindist.xvg" is smaller then one Angstrom. > Is this for the CA-only trajectory? > I think the "g_mindist" command has a bug. In the trajectory each residue is > only represented by a single CA atom (to reduce storage footprint and > increase speed), can it be that g_mindist requires that the atoms have to > "connected" (no broken bonds)? But for calculating the minimal distance of > two groups this should really not be required. > Before we jump to the bug conclusion, can you post the command line you're using, groups you're selecting (are they custom? simply the default "C-alpha"?) and relevant snippets from the output and/or coordinate files that demonstrate a bit better what's going on. If, based on this information, things look weird, then file a bugzilla with files that reproduce the problem. I would disagree that g_mindist requires bond information, since a .tpr file is not strictly required for its function. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 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 Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php
