On Wed, Jun 18, 2014, Jason Swails wrote:
>
> The leapfrog algorithm _is_ used to integrate the equations of motion in
> sander and pmemd.
Since this has come up several times recently: the situation is more complex.
Sander and pmemd integrators are closer to velocity Verlet than to leapfrog,
as the way the kinetic energy is estimated comes from velocity Verlet.
Restart files make things look like leapfrog (for historical reasons).
In terms of roundoff errors, sander and pmemd are neither "pure" leapfrog nor
"pure" velocity Verlet.
Bottom line, if you really care about the differences between leapfrog and vV,
you need to study the code itself.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 18 2014 - 14:00:02 PDT
