[gmx-users] energy xvg file shows a large energy change from time step 0 to time step 0.2 ps

Halie Shah haliepshah at gmail.com
Thu Apr 30 20:45:35 CEST 2009


I have just completed a position restrained dynamics run on my protein with
GROMACS 3.3.3 and I generated an xvg file with the g_energy command...I
noticed in this that the energy for time step 0 was 0.88 (near 0) kj
mol/S-1/N while the energy for time step 0.2ps was 1158....after this the
rest of the time steps (up to 20ps) were roughly around 1150. I'm wondering
why the energy at the start is so low for my protein (which I energy
minimized)...I assumed it would be near 1150. Is this a problem/what does it
mean? Os it fine to move on and do an mdrun?

Thanks so much,
Halie Shah
University of Houston
Briggs Computational Biology Lab
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