[gmx-users] Fatal error (g_polystat)

[Mark Abraham]

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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