[gmx-users] self made topology and fmax

[Mark Abraham]

Joanne Hanna wrote:
> Hi
> 
> I have observed something during em of my molceule using a self made toplogy which may or may not be a problem. Basically my molecule has 27 atoms and during em (using mdrun -v) i get a listing:
> 
> Step=  126, Dmax= 3.1e-04 nm, Epot=  1.42722e+02 Fmax= 1.54906e+02, atom= 80
> 
> This seems very strange as I don't have an atom 80.
> 
> Has anyone ever observed this before or does anyone have any ideas as to what the cause of this is?

Probably you have 80+ atoms :-) The only person who can tell what is 
wrong is the one with your topology and initial structures.

Mark