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

[Justin A. Lemkul]

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?

-Justin

> Thanks so much,
> Halie Shah
> University of Houston
> Briggs Computational Biology Lab
> 
> 
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-- 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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