[gmx-users] TRR file with nstxout= 0

[Steven Neumann]

On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/27/12 11:34 AM, Steven Neumann wrote:
>
>>
>>
>> On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    On 4/27/12 11:22 AM, Steven Neumann wrote:
>>
>>        Dear Gmx Users,
>>
>>        I am running 2 us simulation in implicit solvent model:
>>
>>        define        = -DPOSRES
>>        integrator    = sd        ; leap-frog integrator
>>        nsteps        = 500000000     ; 0.004 * 500000000= 2 us
>>        dt        = 0.004         ; 4 fs
>>        ; Output control
>>        nstxout       = 0
>>        nstxtcout    = 50000        ; xtc compressed trajectory output
>> every 2 ps
>>        nstenergy    = 10000      ; save energies every 2 ps
>>        nstlog        = 10000     ; update log file every 2 ps
>>
>>        How come my trajectory (trr) is being created and takes 80 GB?
>>
>>
>>    The default for nstvout is 100, so you're likely getting very frequent
>>    output of velocities into the .trr file.
>>
>>    -Justin
>>
>> Thank you
>> This job crashed due to the quota exceeded. If change my mdp file (with
>> additional nstvout=0)  using tpbconv and run it from the checkpoint file
>> it
>> should work then with no trr file?
>>
>
> If you need to change the .mdp file, you can't use tpbconv; use grompp to
> generate a new .tpr file and submit the new job.


So if I will create new mdp file (with additional nstvout=0 to get rid of
trr files) and use:

mdrun -s new.tpr -cpi last.cpt

Will I continue from the checkpoint?



>  I'm not sure if you can pick up using mdrun -cpi if the settings have
> changed, but you can try.
>

Yes you can, from 4.0 you do not have to specify -append just -cpi file if
the job crashed.



> -Justin
>
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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