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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
