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

[Acoot Brett]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120322/b99d248b/attachment.html>