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 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
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