On 21/07/2011 3:04 AM, Zhuyi Xue wrote:
Hi, there,
I have a edr file that looks containing about 2000 frames based on its
size as well as the result from gmxcheck:
frame: 75151040 (index 0), t: 150302.094
Reading energy frame 2 time 150320.000
Timesteps at t=150310 don't match (7.90625, 10)
Reading energy frame 2000 time 170300.016
Timesteps at t=172690 don't match (10, 5.64062)
Last energy frame read 2240 time 172695.656
Found 2241 frames.
But when I use g_energy to get the temperature of each frame in this
edr file, only 4 frames could be extracted, the last 10 lines of the
result xvg file is as following:
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Temperature"
150302.093750 301.350067
150310.000000 299.902710
150320.000000 303.125641
150330.000000 300.704010
I have tried eneconv to fix it, but no luck. How to could fix it and
get the values for all frames?
The energy file format contains various quantities related to the
running average and running squared deviation. These require the time
step to be the same between each frame. As such, the analysis tools
expect the time step not to change. Some tools get confused if it does
change. eneconv -settime allows you to artificially manipulate the
times, if you think you have a good reason for concatenating the
energies from dislocated chunks of a trajectory. As soon as you do so,
the averages and fluctuations reported by g_energy are wrong.
Doing restarts with mdrun -append in the manner suggested on the GROMACS
webpage will avoid needing to deal with any of this stuff.
Mark
Another question is what does it mean that the timesteps at t=...
don't match? Will it affect the result of eneconv when connecting
multiple edr files?
Thank you
Zhuyi
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