[gmx-users] a question related to energy minimization "mdrun -v -deffnm em"

[Peter C. Lai]

The output of energy minimization displays the atom with the highest forces
on it for that particular step. It does not reflect the size of the system.

On 2012-03-22 12:09:15AM -0700, Acoot Brett wrote:
> Dear All,
>  
> I am running energy minimization "mdrun -v -deffnm em". The number of atoms in my system is far more than 4018, especially after the water box edded.
>  
> However in the "mdrun -v -deffnm em" running process, the screen shows "Step=  816, Dmax= 1.9e-02 nm, Epot= -3.04546e+06 Fmax= 1.54937e+04, atom= 4018".
>  
>  
> Will you please tell me why the atom number is only 4018? Have I done something wrong?
>  
> Cheers,
>  
> Acoot

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Peter C. Lai			| University of Alabama-Birmingham
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