[gmx-developers] Re: Shift for MARTINI force field

Berk Hess hess at cbr.su.se
Thu Oct 22 09:07:35 CEST 2009

Michael Shirts wrote:
> Good discussion!
>>>> Unfortunately this half step/full step issue will soon be reintroduced
>>>> in Gromacs,
>>>> because the velocity verlet integrator uses full time step velocities
>>>> for coupling.
>>> This might not be a good idea! Can't you leave leap frog?
>> Velocity-verlet is an additional option, it will not replace leap-frog.
>> This issue by itself is enough for me to prefer leap-frog in nearly all
>> cases.
> It's very possible to use an average kinetic energy temperature
> control in velocity verlet -- but to do it in the full Trotter
> formalism may require iterating over the constraints.  Leapfrog gets
> away with this currently by using a linear approximation that isn't
> measure preserving (but is reversible).  I'm trying to figure out if
> it can be done w/o iterating over constraints right now; I'll probably
> wait on this until the velocity verlet framework passes Berk's
> approval -- I'm tired of always updating my local code to match
> rapidly changing Gromacs :)  But certainly both leapfrog and velocity
> verlet would both be options until there's conclusive evidence that
> one is better than the other in all circumstances; right now, there's
> different situations where one or the other may be useful.
>>> I don't see any reason for having the option to output the full step
>>> kinetic energy,
>>> except for exact comparison against more incorrect results.
> See, I would argue that by allowing a comparison vs more inaccurate
> results in the same code base, it makes it easier to prove it's their
> code that's wrong, not Gromacs.  So I'd argue for putting a switch in,
> but turned off by default, and with a warning printed explaining the
> issues.
> Best,
> Michael
That's a good idea.
We can easily put in a environment variable that prints both temperatures
with LF and VV. I would rather not have it an mdp option, since that would
probably cause more confusion for novice users that do good for experts
that would want to check things.
We'll wait with this though until your VV code is in git master, since this
will cause changes to the Ekin code and the energy output.


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