[gmx-users] mdrun append problem

[Chandan Choudhury]

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.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Mon, Feb 8, 2010 at 5:21 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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