[gmx-users] Restart after crash

[Roshan Shrestha]

I had restarted my crash run after around 271 ps. The simulation ran fine
after that and showed










*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:

*gmx energy -f npt.edr -o pressure.xvg*
It shows,
















*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
Tot-Drift-------------------------------------------------------------------------------Pressure
0.791936        2.2    148.261   -8.80046  (bar)*

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