[gmx-developers] stuff in double precision
dmobley at gmail.com
Mon Feb 5 21:13:43 CET 2007
> OK, let me rephrase, it may not be an ill-posed problem, but say you
> make the system 10 times larger, with automatically ten times larger
> energies in absolute numbers, then the maximum accuracy by definition
> becomes 1 kJ/mol, even if you have perfect convergence. From this is
> logically follows that accurate absolute free energy calculation for
> very large systems can not be obtained when using single precision
> So a possible workaround would be to
> - only use the free energy code
> - use double precision summation in the free energy loops only (you want
> to play, you got to pay...)
> This means normal MD is not affected, and only one or a few routines
> have to be altered.
OK, this makes sense, I think -- although the other thing to think
about is that Erik was (is?) working on the ability to evaluate and
output the potential energy of a particular snapshot at several
different lambda values from one simulation to allow the use of
methods like WHAM and BAR for analysis of free energy calculations. We
want to make sure that we're able to maintain precision so that we can
subtract the potential energies from these after they are output and
still have sub-kJ/mol accuracies.
I guess if this means we have to go to double precision for the whole
thing, that's fine -- but if what you're suggesting is a good work
around, it would be great.
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> gmx-developers mailing list
> gmx-developers at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
More information about the gromacs.org_gmx-developers