[gmx-users] Fatal error (g_polystat)

[Chandan Choudhury]

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Fri, Dec 24, 2010 at 3:13 AM, Mark Abraham <Mark.Abraham at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101224/d6452dab/attachment.html>