Thank you very much, that was a good idea! I tried ~/gromacs-4.0.4/bin/trjconv -f dmpc.trr -e 150000 -o dmpc-150ns.trr to get the first 150 ns out of the simulation. Trjconv writes this to me:
Will write trr: Trajectory in portable xdr format trn version: GMX_trn_file (single precision) -> frame 4210 time 42110.004 -> frame 4000 time 40010.000 ------------------------------------------------------- Program trjconv, VERSION 4.0.4 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file ------------------------------------------------------- When checking the new .trr file by ~/gromacs-4.0.4/bin/gmxcheck -f dmpc-150ns.trr the output is: Checking file dmpc-150ns.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 10.000 # Atoms 35513 Reading frame 4000 time 40010.000 Item #frames Timestep (ps) Step 4220 10 Time 4220 10 Lambda 4220 10 Coords 4220 10 Velocities 4220 10 Forces 0 Box 4220 10 So this means that the .trr only conatins 42.2 ns, right? Best, Sarah -----Original Message----- From: [email protected] on behalf of [email protected] Sent: Tue 09-02-2010 16:38 To: [email protected] Subject: [gmx-users] Closing of .trr and .edr files after running out ofspace trjconv -e for the .trr eneconv -e for the .edr --original message -- Dear gmx-users, I have been very unfortunate (and stupid): I was running a simulation of 220 ns and due to limited space at our cluster-computer I was writing the .trr file and .edr file directly to another disc. That was un-clever since I did not write the .cpt file to that disc as well. As I am not the only one using the storage disc it ran out of space very shortly before the end of my simulation and I got this error message in the .log file: Epot (kJ/mol) Coul-SR LJ-SR Coul-14 LJ-14 DMPC-DMPC 2.60809e+02 2.19979e+02 3.95442e+02 7.50289e+01 DMPC-SOL 6.74362e+02 2.11485e+02 0.00000e+00 0.00000e+00 SOL-SOL 9.65717e+02 6.15314e+02 0.00000e+00 0.00000e+00 T-DMPC T-SOL 2.81532e+00 1.30102e+00 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.4 Source code file: enxio.c, line: 212 File input/output error: Cannot close energy file; it might be corrupt, or maybe you are out of quota? ------------------------------------------------------- I guess it is unable to close due to a lack of space? When running gmxcheck on the generated .trr file this message was printed: Checking file dmpc.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 10.000 # Atoms 35513 Reading frame 4000 time 40010.000 ------------------------------------------------------- Program gmxcheck, VERSION 4.0.4 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file ------------------------------------------------------- This .trr file should be 220 ns and 18 G big, it is now 15 G. Even though the .cpt file is only set to update every 15 min (default) there is only 3 min between state_previous.cpt and state.cpt. I think it is because it wrote a new .cpt just when finishing the run? But then non of the .cpt files are "old" enough to allow rerun from the point of the problem. Stupid of me. Now, the simulations was supposed to be of 220 ns, but actually I only need around 150 ns for my purpose. So my question is whether there is anyy way to "close" the .trr file at the point it is at and then have a functional .trr file? Best regards, Sarah -- 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 -- 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
