-- Chandan kumar Choudhury NCL, Pune INDIA
On Fri, Dec 24, 2010 at 3:13 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > 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 time 0.000 # Atoms 162 Last frame 300000 time 30000.002 Item #frames Timestep (ps) Step 300001 0.1 Time 300001 0.1 Lambda 300001 0.1 Coords 300001 0.1 Velocities 300001 0.1 Forces 0 Box 300001 0.1 > 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 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.* > ------------------------------------------------------- > > > 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 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 >
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