[gmx-users] Fatal error (g_polystat)
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 time0.000 * *---* *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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Fatal error (g_polystat)
On 24/12/2010 4:58 AM, Chandan Choudhury wrote: 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*). That looks like subset creation, not concatenation. Perhaps you should clarify what you think should be in all these files, and confirm with gmxcheck. 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 time0.000 / /---/ /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./ --- This means the contents of at least two of the .trr, .tpr and .ndx aren't describing the same thing. Mark 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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Fatal error (g_polystat)
-- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Dec 24, 2010 at 3:13 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/12/2010 4:58 AM, Chandan Choudhury wrote: 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*). That looks like subset creation, not concatenation. Perhaps you should clarify what you think should be in all these files, and confirm with gmxcheck. Sorry. I wrongly copied the commands. The correct command was *trjcat -f 0-20.trr 20-30/20-30.trr -o analysis/0-30/0-30.trr -nice 0* *gmxcheck -f pbc_whole.trr *outputs Checking file pbc_whole.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 162 Last frame 30 time 3.002 Item#frames Timestep (ps) Step310.1 Time310.1 Lambda 310.1 Coords 310.1 Velocities 310.1 Forces 0 Box 310.1 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 time0.000 * *---* *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.* --- This means the contents of at least two of the .trr, .tpr and .ndx aren't describing the same thing. Mark 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 -- gmx-users mailing listgmx-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 listgmx-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
