[gmx-users] problem with .edr file

[Anna Marabotti]

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.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
mosquito"
 
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