[gmx-users] How does MDrun number atoms?

Berk Hess gmx3 at hotmail.com
Thu Jan 15 11:42:45 CET 2009


Could you mail the exact lines in the output which tell you this?
In the energy minimization the atom count should start at 1.
Which version of Gromacs are you using?


> Date: Wed, 14 Jan 2009 14:13:57 -0800
> From: ttrudeau at uvic.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] How does MDrun number atoms?
> 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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