Hi Alan,
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:
http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049137.html
http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049152.html
Ran.
Alan wrote:
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
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.
Thanks,
Alan
--
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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