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

Acoot Brett acootbrett at yahoo.com
Thu Mar 22 08:09:15 CET 2012

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?
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