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

Peter C. Lai pcl at uab.edu
Thu Mar 22 08:12:41 CET 2012

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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