[gmx-users] mdrun append problem

[Justin A. Lemkul]

Chandan Choudhury wrote:
> Hello gmxusers  !!
> 
> gmxcheck on #spc_25_eq.trr prints: (#spc_25_eq.trr is the renamed from 
> #spc_25_eq.trr.1#. mdrun was stopped due to insufficient space)
> 
> Checking file #spc_25_eq.trr
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time 2000.000
> # Atoms  33885
> Reading frame     200 time 3000.000
> WARNING: Incomplete frame: nr 214 time 3070
> 
> 
> Item        #frames Timestep (ps)
> Step           214    5
> Time           214    5
> Lambda         214    5
> Coords         214    5
> Velocities     214    5
> Forces           0
> Box            214    5
> 
> on restarting the mdrun from state.cpi
> 
> mdrun -s spc_25_eq.tpr -cpi state.cpi -c  spc_25_eq.pdb -o spc_25_eq.trr 
> -e spc_25_eq.edr -g spc_25_eq.log  -append yes
> 
> 
> gmxcheck on spc_25_eq.trr prints:
> 
> Checking file spc_25_eq.trr
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time 2000.000
> # Atoms  33885
> Last frame         13 time 2065.000
> 
> 
> Item        #frames Timestep (ps)
> Step            14    4.99999
> Time            14    4.99999
> Lambda          14    4.99999
> Coords          14    4.99999
> Velocities      14    4.99999
> Forces           0
> Box             14    4.99999
> 
> It seems that the -append command didn't append. How can the appending 
> be done.  
> 

What time does "state.cpi" correspond to?  You can use gmxcheck for that.  If 
you're taking up from the original time point, then you won't get continuation. 
  Further, above, you checked "#spc_25_eq.trr" no "spc_25_eq.trr" - are you sure 
you've got all your file names correct?  The combination of -cpi -append should 
work quite well, although I think there are still some issues with file sizes 
 >2GB, but that does not appear to be the case here (you would've gotten a fatal 
error).

-Justin

> 
> Chandan
> 
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> 

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

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