[gmx-users] problem with .edr file

Berk Hess gmx3 at hotmail.com
Mon Sep 13 19:36:31 CEST 2010


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.


Date: Mon, 13 Sep 2010 09:59:43 +0200
From: anna.marabotti at isa.cnr.it
To: gmx-users at gromacs.org
Subject: [gmx-users] problem with .edr file

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 
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 
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, 
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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