[gmx-users] about SHAKE, SETTLE, LINCS and double x single precision
r.friedman at bioc.uzh.ch
Fri May 14 09:52:37 CEST 2010
I don't think using single precision is much of a problem when using
thermostats, regardless of the constraint on the water.
See also Berks' comments:
> Hi there,
> From what I've read and known, here in the list as well, one of the
> main reasons why Gromacs run in single precision is because it has
> LINCS, besides SHAKE, which I believe requires double precision for
> I am drawing such conclusion (that can be wrong) partially based on
> Lippert, R. A., Bowers, K. J., Dror, R. O., Eastwood, M. P.,
> Gregersen, B. A., Klepeis, J. L., Kolossvary, I., and Shaw, D. E. A
> common, avoidable source of error in molecular dynamics integrators.
> Journal of Chemical Physics 126, 4 (Jan. 2007), 046101–1–046101–2
> However, in this letter article they didn't test with LINCS. I would
> love to hear some comments from Gromacs developers.
> When I started in MD, developing our own MD software, all was done in
> double precision, then came Gromacs blowing up this paradigm. (I am
> aware that even in Gromacs, there are routines that really requires
> double precision, e.g. normal mode analysis).
> Essentially I would like to understand better this double x single
> approach in MD re accuracy.
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
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