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

Justin A. Lemkul jalemkul at vt.edu
Fri May 1 13:43:19 CEST 2009

Halie Shah 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?

You'll have to be more specific about what's going on.  Saying "energy" isn't 
very informative.  What were you looking at - potential, total, kinetic?  Are 
you generating velocities at the outset of the simulation?


> Thanks so much,
> Halie Shah
> University of Houston
> Briggs Computational Biology Lab
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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