[gmx-users] TRR file with nstxout= 0

[Steven Neumann]

On Mon, Apr 30, 2012 at 9:39 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 30/04/2012 6:34 PM, Steven Neumann wrote:
>
>
>
> 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.
>
>
> Yes, that will be the effect of the (default) mdrun -append yes in 4.5
>
>
>  Can I then somehow connect those two xtc trajectories using trjconv?
>
>
> Yes, or better trjcat. Be sure to read and understand their -h output
> first.
>
>
>  Which tpr file I should use?
>
>
> You don't even need a .tpr file to concatenate trajectory files.
>
> Mark
>
> Thank you Mark!

Steven

>
> 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
>>
>> ========================================
>> --
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>
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