Hi all, For posterity, in case someone else searches the list with this problem:
The behavior I described a few days ago appears to be related to a bug in gmx_mindist.c related to the precedence of the ternary "?:" operator. g_mindist will fail to emit (to the -o file) an atom pair of minimum/maximum distance when the first atom involved happens to be the first atom of the topology. I've created an issue and submitted a patch: http://redmine.gromacs.org/issues/872 Cheers, MZ On Thu, Jan 26, 2012 at 12:32 PM, Matthew Zwier <mczw...@gmail.com> 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
