Hi, There is no problem at all and you only got notices, not errors. In Gromacs version 4.0 and before each frame in an energy file always contained the energy averages over the whole simulation up to the current step. For proper checkpointing we therefore had to write an energy energy file frame every time a checkpoint is written. The frames cause no problems and all, and g_energy ignores them by default.
Starting with version 4.5 energy frames only contain the average starting from the time when the previous frame was written and we could get rid of the inelegant (bug harmless) extra frames. Note that the energy file that you obtained from the rerun does not have the exact averages and fluctuations with statistics over all md steps. Berk Date: Mon, 13 Sep 2010 09:59:43 +0200 From: anna.marabo...@isa.cnr.it To: gmx-users@gromacs.org Subject: [gmx-users] problem with .edr file Dear gmx-users, I launched several dynamics with gromacs 4.0.7, they finished regularly with apparently no problems (=no error messages at the end of the runs), but when I started analyzing the results, I found a problem in the .edr files. In details, when I used them with g_energy, I found that only 4 of the points that should have been saved as I stated in the .mdp file ( I set to save energy, force, coordinates, log every 100 ps) were present in the file. The .log files were correct and I can see energies in all the steps. I checked both the .trr and the .edr files with gmxcheck and I found that the .trr (and also the .xtc) files were correct, whereas the .edr files gave me the following message error: Checking energy file FAPP2-GLTPapo_md20ns1.edr Opened FAPP2-GLTPapo_md20ns1.edr as single precision energy file frame: 60000 (index 0), t: 120.000 Reading energy frame 2 time 300.000 Timesteps at t=200 don't match (80, 100) Reading energy frame 200 time 20100.000 Timesteps at t=20100 don't match (100, 20) Last energy frame read 201 time 20120.000 Found 202 frames. I used mdrun -rerun and the .trr file to obtain a new .edr file, and this time the file was correct, with all the points present, so I think that the run was made correctly, but the .edr was not properly saved. I don't know why this happened: do you think it could be a problem in the Gromacs version, or in the Gromacs installation? Any hint will be very appreciated. 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 (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito" -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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