[gmx-users] TRR file with nstxout= 0

[Steven Neumann]

On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>


Indeed, it complains in terms of not present trr file (3 out of 4 files
present) and he does not want to carry on. But when I change name of the
output it starts from the checkpoint  generating new files. Can I then
somehow connect those two xtc trajectories using trjconv? Which tpr file I
should use?

Steven



>
> --
> ==============================**==========
>
> 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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