[gmx-users] problem with .edr file

Anna Marabotti anna.marabotti at isa.cnr.it
Mon Sep 13 09:59:43 CEST 2010

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 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.marabotti at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100913/39082f20/attachment.html>

More information about the gromacs.org_gmx-users mailing list