Just to mention that for a reference, I am drawing partially conclusions
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
Alan
On Thu, May 13, 2010 at 16:04, Alan <alanwilter.gmail.com> wrote:
> Hi there,
>
> From what I've read and known, here in the list as well, one of the main
> reasons why sander/pmemd demands double precision is SHAKE (at least from
> the pmemd.cuda point of view).
>
> Reading Amber11 manual and I verified that Amber uses only SHAKE, no
> SETTLE, no LINCS, nothing else.
>
> I saw the discussions here about double/single precision or even hybrid
> precision (just reading about Anton, from Shaw's group).
>
> 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).
>
> I am starting this discussion here but I post in Gromacs list too, but
> essentially I would like to understand better this double x single approach
> in MD re accuracy. And of course correct what I said in the 1st paragraph
> since I may be wrong in my assertion.
>
> 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<<
>
--
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<<
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Received on Thu May 13 2010 - 08:30:06 PDT
