[gmx-users] Re: Re; Failed Energy Minimization (solved!)

Justin M. Shorb shorb at wisc.edu
Fri Apr 20 21:02:45 CEST 2007

Greetings everyone!

After trying my same shell scripts on another computer, using single 
precision, I have worked out that the double precision version of 
Gromacs-3.3.1 does not energy minimize consistently. The exact same run 
script using different force fields will energy minimize sometimes, but 
most force fields give infinite forces. This was verified for 
diglycine, trialanine, alanine dipeptide as well as a very large 
protein. In fact, the exact same run script for diglycine gives 
minimization within 8 steps for single precision, where with double 
precision it had infinite forces (for no reason) in step 0. I even 
wrote a quick script to determine the nearest neighbors for each atom, 
and found that all atoms were at least 0.9 Angstrom apart (so no 

Recompiling the exact same source code in single precision on my own 
machine reproduced the success identically. Thus I am left to believe 
that there is bug in the double precision version of the energy 
minimization (mdrun_d or grompp_d, I don't know) code.

Just thought I would let everyone know to avoid double precision when 
running energy minimization.

Thanks for all your suggestions!

Justin M. Shorb			Phone: (608) 262-0483
Skinner Group				shorb at wisc.edu
University of Wisconsin-Madison,  Department of Chemistry
1101 University Ave., Madison, WI, 53706

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