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Hi,<br><br>There is no problem at all and you only got notices, not errors.<br>In Gromacs version 4.0 and before each frame in an energy file always contained the energy averages<br>over the whole simulation up to the current step. For proper checkpointing we therefore had to write<br>an energy energy file frame every time a checkpoint is written. The frames cause no problems and all,<br>and g_energy ignores them by default.<br><br>Starting with version 4.5 energy frames only contain the average starting from the time when the previous<br>frame was written and we could get rid of the inelegant (bug harmless) extra frames.<br><br>Note that the energy file that you obtained from the rerun does not have the exact averages and fluctuations<br>with statistics over all md steps.<br><br>Berk<br><br><hr id="stopSpelling">Date: Mon, 13 Sep 2010 09:59:43 +0200<br>From: anna.marabotti@isa.cnr.it<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] problem with .edr file<br><br>
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<div><font face="Arial" size="2"><span class="ecx214194907-13092010">Dear
gmx-users,</span></font></div>
<div><font face="Arial" size="2"><span class="ecx214194907-13092010">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:</span></font></div>
<div><font face="Arial" size="2"><span class="ecx214194907-13092010"></span></font> </div>
<div><font face="Arial" size="2">Checking energy file
FAPP2-GLTPapo_md20ns1.edr</font></div>
<div> </div>
<div><font face="Arial" size="2">Opened FAPP2-GLTPapo_md20ns1.edr as single
precision energy file<br>frame: 60000 (index
0), t: 120.000<br>Reading energy
frame 2 time 300.000<br>Timesteps at t=200
don't match (80, 100)<br>Reading energy frame 200 time
20100.000<br>Timesteps at t=20100 don't match (100, 20)<br>Last energy frame
read 201 time 20120.000</font></div>
<div> </div>
<div><font face="Arial" size="2">Found 202 frames.</font></div>
<div> </div>
<div><font face="Arial" size="2"><span class="ecx214194907-13092010">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.</span></font></div>
<div><font face="Arial" size="2"><span class="ecx214194907-13092010">Many thanks in
advance and best regards</span></font></div>
<div><font face="Arial" size="2"><span class="ecx214194907-13092010">Anna</span></font></div>
<div align="left"><font face="Arial" size="2">____________________________________________________</font></div>
<div align="left"><font face="Arial" size="2">Anna Marabotti, Ph.D.</font></div>
<div align="left"><font face="Arial" size="2">Laboratory of Bioinformatics and
Computational Biology</font></div>
<div align="left"><font face="Arial" size="2">Institute of Food Science,
CNR</font></div>
<div align="left"><font face="Arial" size="2">Via Roma, 64</font></div>
<div align="left"><font face="Arial" size="2">83100 Avellino (Italy)</font></div>
<div align="left"><font face="Arial" size="2">Phone: +39 0825 299651</font></div>
<div align="left"><font face="Arial" size="2">Fax: +39 0825 781585</font></div>
<div align="left"><font face="Arial" size="2">Email: <a href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</a></font></div>
<div align="left"><font face="Arial" size="2">Skype account: annam1972</font></div>
<div align="left"><font face="Arial" size="2">Web page: <a href="http://bioinformatica.isa.cnr.it/anna/anna.htm" target="_blank">http://bioinformatica.isa.cnr.it/anna/anna.htm</a></font></div>
<div align="left"><font face="Arial" size="2"></font> </div>
<div align="left"><font face="Arial" size="2">"If you think you are too small to make
a difference, try sleeping with a mosquito"</font></div>
<div> </div>
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