[gmx-users] FW: trjconv -dump problem

[Ehud Schreiber]

Dear Gromacs users,

 

I minimized a protein structure 1IARcompleted_WT.pdb, getting, among
others, the files 1IARcompleted_WT_minimized.trr and
1IARcompleted_WT_minimized_potential_energy.xvg . Looking at the latter
file showed the last frame to be at 217 ps:

 

.

.

@    title "Gromacs Energies"

@    xaxis  label "Time (ps)"

@    yaxis  label "(kJ/mol)" 

.

.

@ s0 legend "Potential"

    0.000000  -31997.519531

    0.000000  -33810.406250

  200.000000  -69850.609375

  217.000000  -69898.031250

 

I wanted to extract only this last frame from the .trr file, so used

 

trjconv  -f 1IARcompleted_WT_minimized.trr -o
1IARcompleted_WT_minimized_217.trr -dump 217

 

However, this seems to have produced a file with the t = 200 ps
conformation, though the dump parameter was recorded, as trjconv output
was:

 

.

.

Option       Type   Value   Description

------------------------------------------------------

.

.

-dump        time   217     Dump frame nearest specified time (ps)

.

.

Will write trr: Trajectory in portable xdr format

trn version: GMX_trn_file (single precision)

Reading frame       2 time  200.000   

Dumping frame at t= 200 ps

Reading frame       3 time  217.000   

.

.

 

Also, using -dump 200 gave an identical file to the above.

 

Any idea why the expected timeframe isn't reproduced?

I'm using gromacs 4.5.3.

 

Thanks,

Ehud Schreiber.

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120214/e029e904/attachment.html>