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

Pawan Kumar pawan.chinari at gmail.com
Fri May 1 06:26:19 CEST 2009


It will be better to check the energy after the final production run ....


On Fri, May 1, 2009 at 12:15 AM, Halie Shah <haliepshah at gmail.com> wrote:

> Hi!
> 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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