Dear gmx-users, since I'm sending my simulations to a system with a queue with a wallclock time of 24 h, I necessarily have to simulate small parts of my simulation, that I "stick" together at the end with trjconv. To continue my simulations, I'm using the .cpt file. Here my settings concerning the number of steps, dt etc. Since I started the full MD after 20 ps NVT and 100 ps NPT I set the mdp file as: integrator = md dt = 0.002 nsteps = 2500000 (total 5 ns - the max time compatible with the wallclock time) init_step = 70000 (the last step after NVT+NPT) tinit = 0 nstxout,vout,fout,log,energy: 50000 In the command to launch the MD simulation I set: mpirun -np 32 -s 1R3Afull.tpr -deffnm 1R3Afull -cpt 60 After the first 5 ns of simulation, I obtained all the files expected, and I extended the trajectory of further 5 ns using the command: tpbconv -s 1R3Afull.tpr -extend 5000 -o 1R3Afull2.tpr and mpirun -np 32 -s 1R3Afull2.tpr -cpi 1R3Afull.cpt -deffnm 1R3Afull2 -cpt 60 I repeated the procedure until I obtained 20 ns trajectory. Then, I used trjcat to concatenate 1R3Afull.xtc + 1R3Afull2.xtc + 1R3Afull3.xtc + 1R3Afull4.xtc creating 1R3Afull20ns.xtc and eneconv to do the same with 1R3Afull.edr + 1R3Afull2.edr + 1R3Afull3.edr + 1R3Afull4.edr, creating 1R3Afull20ns.edr. Then, I used gmxcheck -e 1R3Afull20ns.edr to check the final .edr file. I obtained an error message: Checking energy file 1R3Afull20ns.edr Opened 1R3Afull20ns.edr as double precision energy file frame: 0 (index 0), t: 140.000 Reading energy frame 2 time 300.000 Timesteps at t=200 don't match (60, 100) Reading energy frame 50 time 5100.000 Timesteps at t=5100 don't match (100, 40) Timesteps at t=5140 don't match (40, 60) Timesteps at t=5200 don't match (60, 100) Reading energy frame 100 time 10000.000 Timesteps at t=10100 don't match (100, 40) Timesteps at t=10140 don't match (40, 60) Timesteps at t=10200 don't match (60, 100) Reading energy frame 150 time 14900.000 Timesteps at t=15100 don't match (100, 40) Timesteps at t=15140 don't match (40, 60) Timesteps at t=15200 don't match (60, 100) Last energy frame read 198 time 19600.000 Found 199 frames. gcq#131: "Royale With Cheese" (Pulp Fiction)
I don't understand why there are so many mismatches in my file. Moreover all but one are in the correspondence of the "junctions" I made between two consecutive 5 ns runs. Does it depend on some settings regarding init_step or dt or tinit in the .mdp file? Did I make correctly the continuation? Could somebody help me to find the error? Many thanks in advance and best regards Anna __________________________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with the gun is a dead man" (Roberto Benigni, about Roberto Saviano)
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