[gmx-users] Re: inconsistent energy drops

[Justin Lemkul]

On 8/1/13 4:58 PM, Brad Van Oosten wrote:
> I used the mdrun -rerun option to recalculate the energies of the system and
> it gave me nearly the same energy plot but without the random drops(see plot
> below).  I am still unsure what is causing the jumps but i do not believe it
> is from my system.  Since the energy is used in the calculation for the next
> step, is there reason to worry about the validity of this run?
>

Forces dictate the dynamics, not the energies.  This could be either a dynamics 
bug or an output bug.

> potential energy (black being the original potential and red being the
> -rerun)
> <http://gromacs.5086.x6.nabble.com/file/n5010294/pot_rerun.png>
> Zoomed in on first peaks:
> <http://gromacs.5086.x6.nabble.com/file/n5010294/pot_rerun_close.png>
>

OK, that does look weird.  What Gromacs version is this?  What is in your .mdp file?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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