[gmx-users] Restart after crash

[Mark Abraham]

Hi,

You'll have to look inside your log files to find out what mdrun decided it
was able to do.

Mark

On Tue, Oct 4, 2016 at 5:21 AM Roshan Shrestha <roshanpra at gmail.com> wrote:

> I had restarted my crash run after around 271 ps. The simulation ran fine
> after that and showed
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> *starting mdrun 'Protein in water'2500000 steps,   5000.0 ps (continuing
> from step 135600,    271.2 ps).step 2499900, remaining wall clock time:
> 1 s          Writing final coordinates.step 2500000, remaining wall clock
> time:     0 s                         Core t (s)   Wall t (s)
> (%)       Time:   180030.312    45575.364
> 395.0                         12h39:35                 (ns/day)
> (hour/ns)Performance:        8.965        2.677*
> However, while plotting pressure when I used this command:
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> *gmx energy -f npt.edr -o pressure.xvg*
> It shows,
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> *Reading energy frame    300 time  300.000         WARNING: there may be
> something wrong with energy file npt.edrFound: step=0, nre=0, nblock=0,
> time=0.Trying to skip frame expect a crash thoughWARNING: there may be
> something wrong with energy file npt.edrFound: step=0, nre=0, nblock=0,
> time=0.Trying to skip frame expect a crash thoughLast energy frame read 353
> time    0.000         Statistics over 175501 steps [ 0.0000 through
> 351.0000 ps ], 1 data setsAll statistics are over 1756
> pointsEnergy                      Average   Err.Est.       RMSD
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> Tot-Drift-------------------------------------------------------------------------------Pressure
> 0.791936        2.2    148.261   -8.80046  (bar)*
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> So, they are collecting data for only around 351 ps while my simulation was
> for 5000 ps. It says a problem with my npt.edr file, but I could not figure
> out why and how since my simulation ran fine. I want to get data sets from
> all the simulation time (5000 ps). Thanks
>
>
> --
> Roshan Shrestha
> Graduate Student
> Central Department of Physics,Tribhuvan University
> Kathmandu,Nepal
> --
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