Hello all !! I have a 30 ns trajectory in two parts (0-20 & 20-30). I am using Gromacs 4.0.7. I concatenated using trjcat (*echo 2 | trjconv -s md10-30.tpr -f 0-30.trr -o pbc_whole.trr -n index_grdf.ndx -nice 0*). Then I converted the concatenated trajectory into pbc trajectory using trjconv (*echo 2 | trjconv -f 0-30.trr -s md10-30.tpr -o pbc_whole.trr -n index_grdf.ndx -pbc whole*). The problem comes when I try to use the g_polystat utility (*echo 2 |* *g_polystat -s md10-30.tpr -f pbc_whole.trr -n index_grdf.ndx -o polystat_pbc.dat -xvgr*). The error message it produces is : *trn version: GMX_trn_file (single precision)* *Reading frame 0 time 0.000 * *-------------------------------------------------------* *Program g_dist, VERSION 4.0.7* *Source code file: mshift.c, line: 103* * * *Fatal error:* *Molecule in topology has atom numbers below and above natoms (162).* *You are probably trying to use a trajectory which does not match the first 162 atoms of the run input file.* *You can make a matching run input file with tpbconv.* -------------------------------------------------------
The same error message erupts when I try to use g_dist. (echo "5 24" | g_dist -f pbc_whole.trr -s md10-30.tpr -n index_grdf.ndx -o dist_N-N.xvg). But when I execute g_mindist (echo "5 24" | g_mindist -f pbc_whole.trr -s md10-30.tpr -n index_grdf.ndx -o mindist_N-N.xvg). I works w/o any error message. Can figure out the probable cause. Please help. -- Chandan kumar Choudhury NCL, Pune INDIA
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