[gmx-users] Re: Re; Failed Energy Minimization (solved!)
lindahl at cbr.su.se
Fri Apr 20 21:20:03 CEST 2007
Double precision energy minimization works great for us, so if you
have system where you think there _might_ be a bug, please submit it
In fact, you should always use double precision l-bfgs mimimization
prior to normal mode analysis, IMHO...
On Apr 20, 2007, at 9:02 PM, Justin M. Shorb wrote:
> 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 overlap).
> 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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