[gmx-users] mdrun append problem

[Justin A. Lemkul]

Chandan Choudhury wrote:
> Dear Justin
> Thanks for your reply. 
> I didnot get any fatal error. Since, the mdrun has started (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 ), it has created new 
> state.cpi. So I now I cannot verify it. >From now, I will definetly 
> check the .trr and .cpi before issuing the append command. 
> And I thing, does the value of - append i.e 'yes' is compulsion for 
> appending or just -append would work? I am asking this because once I 
> restartd mdrun as -cpi state.cpi -append, with no 'yes' value to mdrun. 
> It then created new gro, trr and edr files. What I found here was the 
> .trr (generated using cpi flag) file had all the frames.
> 

You only need to use -append.  Booleans do not need "yes" to follow.

-Justin

> Chandan
> 
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> 
> 
> On Mon, Feb 8, 2010 at 5:21 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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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

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