Dear Justin Thanks for your reply. I didnot get any fatal error. Since, the mdrun has started (mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr -e spc_25_eq.edr -g spc_25_eq.log -append yes ), it has created new state.cpi. So I now I cannot verify it. From now, I will definetly check the .trr and .cpi before issuing the append command. And I thing, does the value of - append i.e 'yes' is compulsion for appending or just -append would work? I am asking this because once I restartd mdrun as -cpi state.cpi -append, with no 'yes' value to mdrun. It then created new gro, trr and edr files. What I found here was the .trr (generated using cpi flag) file had all the frames.
Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 5:21 PM, Justin A. Lemkul <[email protected]> wrote: > > > Chandan Choudhury wrote: > >> Hello gmxusers !! >> >> gmxcheck on #spc_25_eq.trr prints: (#spc_25_eq.trr is the renamed from >> #spc_25_eq.trr.1#. mdrun was stopped due to insufficient space) >> >> Checking file #spc_25_eq.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time 2000.000 >> # Atoms 33885 >> Reading frame 200 time 3000.000 >> WARNING: Incomplete frame: nr 214 time 3070 >> >> >> Item #frames Timestep (ps) >> Step 214 5 >> Time 214 5 >> Lambda 214 5 >> Coords 214 5 >> Velocities 214 5 >> Forces 0 >> Box 214 5 >> >> on restarting the mdrun from state.cpi >> >> mdrun -s spc_25_eq.tpr -cpi state.cpi -c spc_25_eq.pdb -o spc_25_eq.trr >> -e spc_25_eq.edr -g spc_25_eq.log -append yes >> >> >> gmxcheck on spc_25_eq.trr prints: >> >> Checking file spc_25_eq.trr >> trn version: GMX_trn_file (single precision) >> Reading frame 0 time 2000.000 >> # Atoms 33885 >> Last frame 13 time 2065.000 >> >> >> Item #frames Timestep (ps) >> Step 14 4.99999 >> Time 14 4.99999 >> Lambda 14 4.99999 >> Coords 14 4.99999 >> Velocities 14 4.99999 >> Forces 0 >> Box 14 4.99999 >> >> It seems that the -append command didn't append. How can the appending be >> done. >> > > What time does "state.cpi" correspond to? You can use gmxcheck for that. > If you're taking up from the original time point, then you won't get > continuation. Further, above, you checked "#spc_25_eq.trr" no > "spc_25_eq.trr" - are you sure you've got all your file names correct? The > combination of -cpi -append should work quite well, although I think there > are still some issues with file sizes >2GB, but that does not appear to be > the case here (you would've gotten a fatal error). > > -Justin > > > >> Chandan >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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