[gmx-users] TRR file with nstxout= 0

[Justin A. Lemkul]

On 4/27/12 12:09 PM, Steven Neumann wrote:
>
>
> On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
>         <mailto: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?
>

That's the question I posed below...

>       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.
>

I am aware of checkpointing, but what I'm not sure of is if you change output 
options (or others) mid-stream, if the checkpointing mechanism will complain, 
particularly due to the changes in the .trr content.  You'll have to try and see.

-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

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