[gmx-users] about SHAKE, SETTLE, LINCS and double x single precision
alanwilter at gmail.com
Thu May 13 17:27:14 CEST 2010
>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 accuracy.
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.
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