[gmx-users] TRR file with nstxout= 0
s.neumann08 at gmail.com
Fri Apr 27 18:09:38 CEST 2012
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.
>> 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
>> 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 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
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