[gmx-users] Re: inconsistent energy drops

[Brad Van Oosten]

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?

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> 

Thanks, 
Brad



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