Hi Peter, Thanks for the reply. I'm not using the contact information at all (-on is unspecified), and yes, it still generates a result for >6A in the distance output (-od) , but the result for which atoms are at the reported distance is sometimes missing from the atom pair output (-o) file.
MZ On Thu, Jan 26, 2012 at 6:42 PM, Peter C. Lai <p...@uab.edu> wrote: > I have not read the source, but the default search radius for mindist is > 6A. If you have no contacts within 6A of the atoms in the primary group > to the target group for a given frame, will it still generate a result, > since for all intents and purposes the array search should be null in > that case? > > On 2012-01-26 12:32:15PM -0500, Matthew Zwier wrote: >> Hi all, >> >> I'm running g_mindist (from 4.5.5) on a slew of very short >> trajectories (51 frames) in order to obtain both minimum distances and >> the corresponding atom pairs, using >> >> echo 10 11 | g_mindist -nice 10 -f seg.xtc -n $NDX -s $TPR -nopbc -o >> mindist_pairs.out -xvg none >> >> where NDX and TPR are (valid) index and topology files, respectively, >> and nopbc is specified because there is no periodic box (these are >> GB/SA simulations). This is on a 64-bit Linux box, with GROMACS and >> all dependencies compiled with GCC. For all trajectories, the >> resulting mindist.xvg always contains 51 entries with reasonable >> values (in the 1.1-1.5 nm range), but for a subset of the >> trajectories, the corresponding mindist_pairs.out contains less than >> 51 entries (as low as ~30 in some cases). >> >> Reading the source for gmx_mindist.c, it appears that this should >> never occur, at least not without giving a nonsense value of the >> minimum distance for that frame in the process (1 mm, it would appear >> from the source!). I'm either missing something in my reading of >> gmx_mindist.c, I've found a bug (unlikely), or I've managed to >> convince GCC to mis-compile g_mindist somehow (more likely, though >> still somewhat baffling). Can anyone help me figure out what's going >> on? >> >> Cheers, >> Matt Z. >> -- >> 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 > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > 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
