[gmx-users] TRR file with nstxout= 0

[Justin A. Lemkul]

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

-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

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