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