[gmx-users] restarting mdrun

[Justin A. Lemkul]

Chandan Choudhury wrote:
> Hi Mark !!!
> Thanks for answering.
> My query is how do I restart my mdrun because the command
> nohup mpirun -np 16 -machinefile mac mdrun -s md5-10.tpr -cpi state.cpt 
> -append &
> will not start from where the trajectory was stopped (i.e; time 
> 9169.500). As this command will continue the simulation from where the 
> cpt file was written.
> 

Right, it will start from whenever the checkpoint was written.  You should also 
have a state_prev.cpt that is a backup in case this type of thing happens; it 
may help.  Regardless, with a 36-GB .trr file, the -append option will not work. 
  Leave it out and use trjcat later.

-Justin

> Any suggestions??
> 
> chandan
> 
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> 
> 
> On Tue, Feb 16, 2010 at 9:36 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     On 17/02/10 02:52, Chandan Choudhury wrote:
> 
>         Hello gmxusers !!!
>         I want to continue my simulation, from where the point where it
>         stopped.
>         The gmxcheck on .trr and cpt files are as:
> 
>         $gmxcheck -f state.cpt
> 
>         Checking file state.cpt
> 
>         # Atoms  186864
>         Last frame         -1 time 9362.500
> 
> 
>         Item        #frames Timestep (ps)
>         Step             1
>         Time             1
>         Lambda           1
>         Coords           1
>         Velocities       1
>         Forces           0
>         Box              1
> 
>         $gmxcheck -f 5-10.trr
> 
>         Checking file 5-10.trr
>         trn version: GMX_trn_file (single precision)
>         Reading frame       0 time 5169.500
>         # Atoms  186864
>         Reading frame    8000 time 9169.500
> 
> 
>         Item        #frames Timestep (ps)
>         Step          8395    0.5
>         Time          8395    0.5
>         Lambda        8395    0.5
>         Coords        8395    0.5
>         Velocities    8395    0.5
>         Forces           0
>         Box           8395    0.5
> 
> 
>         There is a mismatch of time in both the outputs.
> 
>         The date of modification of both the files as shown are:
> 
>         Feb 15 19:55 state.cpt
> 
>         $date -r 5-10.trr
>         Mon Feb 15 19:59:56 IST 2010
> 
>         The cpt file shows time greater than the trr file. But the time of
>         modification of cpt file is less than trr file.
> 
> 
>     If the simulation stopped catastrophically, then the timestamp could
>     easily differ, especially if the .cpt is opened, written to and
>     closed periodically, and the .trr is open continuously.
> 
> 
>         Cannot understand the,
>         how to restart the mdrun. And the size of the trr file is 36GB.
>         Can I
>         use the append flag in mdrun for gmx 4.0.5.
> 
> 
>     Search the webpage for suggestions.
> 
>     Mark
>     -- 
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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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