[gmx-users] How does MDrun number atoms?

ttrudeau ttrudeau at uvic.ca
Wed Jan 14 23:13:57 CET 2009

Our minimization ended with a large net force on "atom 0." Since there is
no atom 0 in our .gro, .top, or .ndx files, is mdrun re-numbering the
atoms in our system according to some scheme, or is this an indication
that something very wrong is happening?

-Travis Trudeau, MSc. student at University of Victoria

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