[gmx-users] Re: How does MDrun number atoms?

ttrudeau ttrudeau at uvic.ca
Fri Jan 16 01:19:48 CET 2009

We are using version 3.3. We switched over to 4.0.2 but encountered the
'hanging' problem mentioned by Patrick Fuchs and others and went back. Our
version of MPI LAM is 7.1.2. We'll try using openMPI and see if that
allows GMX 4.0.2 to run okay.

By using gmxdump on our .tpr file, we figured out which atom is atom 0.
Thanks Justin!

The exact lines at the end of our minimization were:

"Steepest Descents converged to machine precision in 52 steps,
but did not reach the requested Fmax < 1.
Potential Energy  = -1.09858316637924e+06
Maximum force     =  2.93642571065333e+07 on atom 0
Norm of force     =  4.01374340154852e+07"

-Travis Trudeau

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