[gmx-users] Fatal error (g_polystat)

[Chandan Choudhury]

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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