[gmx-users] Truncation of file traj.trr failed

[Justin A. Lemkul]

ram bio wrote:
> Dear justin,
> 
> The job was terminated as under:
> 
> vol 0.92  imb F  1% step 5860300, will finish Sun Nov 15 06:56:32 2009
> =>> PBS: job killed: walltime 86438 exceeded limit 86400
> mpiexec: killing job...
> 
> i think due to queueing system and maximum time being 24hrs.
> 
> i donot know how to know whether new cpt files are written all the
> files i have are the same 2 cpt files state.cpt and state_prev.cpt.
> 

You will only ever have state.cpt and state_prev.cpt, but the timestamp on the 
file might give you a clue as to when they were written :)

> when i did gmxcheck on both cpt files the output was
> Checking file state.cpt
> 
> # Atoms  31609
> Last frame         -1 time 2928.000
> 
> 
> Item        #frames Timestep (ps)
> Step             1
> Time             1
> Lambda           1
> Coords           1
> Velocities       1
> Forces           0
> Box              1
> 
> for state_prev.cpt
> 
> # Atoms  31609
> Last frame         -1 time 2896.000
> 
> 
> Item        #frames Timestep (ps)
> Step             1
> Time             1
> Lambda           1
> Coords           1
> Velocities       1
> Forces           0
> Box              1
> 
> when the run is extended for the second time do gromacs generate a new
> cpt file i mean with new name or same named files (state.cpt and
> state_prev.cpt) with new check points written..
> 

New checkpoint files are written every -cpt minutes (by default, 15).  It looks 
like your simulation did not continue past 2928 ps, so do check the timestamp on 
all of your output files in case something weird is going on.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================