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<DIV><FONT size=2 face=Arial><SPAN class=214194907-13092010>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=214194907-13092010>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 size=2 face=Arial><SPAN
class=214194907-13092010></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial>Checking energy file
FAPP2-GLTPapo_md20ns1.edr</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial>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 size=2 face=Arial>Found 202 frames.</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=214194907-13092010>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 size=2 face=Arial><SPAN class=214194907-13092010>Many thanks in
advance and best regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=214194907-13092010>Anna</SPAN></FONT></DIV>
<DIV align=left><FONT size=2
face=Arial>____________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science,
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino (Italy)</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Email: <A
href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web page: <A
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"If you think you are too small to make
a difference, try sleeping with a mosquito"</FONT></DIV>
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