[gmx-users] How does MDrun number atoms?

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 14 23:40:46 CET 2009

ttrudeau wrote:
> 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?

Numbering in the .tpr starts from 0 (do a gmxdump to see for yourself).


> -Travis Trudeau, MSc. student at University of Victoria
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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