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
