[gmx-developers] Re: Re: Re: Energy conservation

[Michael Shirts]

Hi, Erik-

> I would agree with Michael here. Using double precision and an extra
> iterations in LINCS I managed to achieve virtually perfect (=no
> measurable drift) over half a microsecond, when using a water system
> that was hacked to disable SETTLE.

Hi, Erik-

I'd love to get the .mdp and .gro for the system to test on my
velocity verlet + Settle + Rattle integrator to see if I can get
comparable performance.   Why do you think it was necessary to comment
out SETTLE?

Also, after going through the integrators, it seems to me that
leapfrog + constraints, as implemented in GROMACS, is actually
equivalent to position verlet -- this is because the velocities are
computed by position differences.  This doesn't actually change the
position trajectories at all, but does lose a bit of precision off the
velocities.  Not sure it's a contributing factor, but though I'd
mention it.

Having the data + standards for these examples in the CVS (or
otherwise posted) would allow other people.  I know there some
regression testing that is done -- is that information (not only the
input files, but the results) in the CVS?  Are the example files in
the CVS the same as the ones used in the regression testing?  I'd also
be hearing from Charlie Peck about how the examples could be better
used from a CS / Quality control perspective to be able to better
ensure a good development process.

Michael Shirts
Research Fellow
Columbia University