[gmx-developers] re: Velocity verlet version of Gromacs with trotter-decomposition NPT

Berk Hess hess at cbr.su.se
Mon Oct 12 18:46:51 CEST 2009

Hi Michael,

Again, thanks a lot for the all the work!

I have looked through the code a bit and it all looks pretty good.
There are a few cosmetic things that have to be changed.
The real work for, mainly for me I'm afraid, is to check that all the other
integrators, thermo/barostats, continuation etc. are not affected.
Also a we probably want all the other thermo and barostats
as well with VV, but that should be little work.

I asked Gerrit to have a look if the global scheme of things
still matches what I discussed with him, so I know what the state
of the simulation is at every point.


Michael Shirts wrote:
>> Sorry for not answering earlier.
>> I have been very busy.
> No worries, I know how that goes!
>> I hope to have time to look into the code in detail next week.
> Sounds good.  Please let me know of any changes that might need to be
> made in the architecture.
>> Thanks for all the effort!
> You're welcome!  Getting this working was a bit of a nightmare,so the
> appreciation is appreciated.
> Note:  I've just checked in a couple more changes so that it runs on
> parallel.  Currently the energies are summed incorrectly with MPI for
> velocity verlet (I'm getting kinetic energies correct, but
> temperatures are scaled by 1/np and potential energies are scaled by
> np), but they are correct for leapfrog.  I'll try to drill down to get
> it correct when I have the opportunity.
> Also, if anyone else wants to try it, the -correct- repository
> location is actually:
> git://git.gromacs.org/~mrshirts/gromacs_mrs.git
> (I'm still getting a hang of git . . .)
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