[gmx-users] Re: energyfile questions

Matteus Lindgren matteus.lindgren at chem.umu.se
Fri Sep 5 18:40:24 CEST 2008

Thanks Justin for the reply. 

Gmxcheck of the .edr file does not tell me the spacing of the frames,
probably because it is inconsistent. I do get a lot of the timesteps don´t
match errors though. It seems all my .edr files that have been calculated on
the cluster have extra frames in the output, while on my workstation it
works fine fro the same .tpr file. Something with data flush on the cluster?

Since this run was the first I used grompp to make the .tpr but it shouldn’t
matter if it’s a cluster only problem.

Checking energy file s6wu.1.edr

Opened s6wu.1.edr as single precision energy file
frame:      0 (index      0), t:      0.000
Reading frame    200 time  100.000
Timesteps at t=120.5 don't match (0.5, 0.00999451)

Timesteps at t=120.51 don't match (0.00999451, 0.490005)
Reading frame    400 time  199.500
Timesteps at t=237 don't match (0.5, 0.0699921)

Timesteps at t=237.07 don't match (0.0699921, 0.430008)
Reading frame    700 time  349.000
Timesteps at t=354 don't match (0.5, 0.0299988)

And so on...

About the protein temperature: Is 50K fluctuation in temperature really ok
for nose-hoover thermostat on a 100 residue protein????


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