[gmx-developers] Various integrator questions

[Berk Hess]

>
>
>Berk said:
>
>>/ I changed the kinetic energy calculation in the CVS from being based on
>/>/ the average of the n-1/2 and n+1/2 velocities to n-1/2 and n+1/2 Ekin.
>/>/ With the old method the discretization error in Ekin (always causing
>/>/ Ekin to be too small) was 4 times larger than with the new code.
>/>/ The error causes the temperature to appear as too low, so the temperature
>/>/ coupling scales it up too much, which effectively results in an ensemble
>/>/ at a too high temperature.
>/
>I'll put in a plug again for Velocity Verlet, which avoids this whole
>issue, as the velocities are determined at the same time as the
>coordinates.  I'll start working on implementing my local version on
>the 3.3 codebase, so that people can check it out.
>
>Best,
>Michael
>

Although by itself correct, there is another issue here.

Although Velocity Verlet avoid kinetic energy and pressure complications,
it introduces complications with the constraint algorithms as the velocities
need to be constrained as well, whereas there are automatically correct 
with leap-frog.
I guess there is no conceptual problem and one can always just constrain
the full-step velocities. But this does involve coding a velocity 
version for all
constraint algorithms. (I have already implemented LINCS code for this).

Berk.