[gmx-developers] Re: re: Velocity verlet version of Gromacs with trotter-decomposition NPT (Berk Hess)

Michael Shirts mrshirts at gmail.com
Tue Oct 13 15:00:37 CEST 2009

Hi, Berk-

> Again, thanks a lot for the all the work!

You're welcome!

> 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.

Absolutely, I'm sure there are.

> 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.

Correct!  I'm happy to test out any combination to make sure that the
results are equivalent.  I tested all the most common integrators, but
if you give me a complete list to check, I can get that done ASAP.  I
know you'd like to test as well, but I can at least go through and
clear the way in case there are any bugs.  I think there's one more
parallel bug with pressure control to fix as well.  Let me know if I
should go ahead with this now, or wait until you fix the cosmetic

> Also a we probably want all the other thermo and barostats
> as well with VV, but that should be little work.

Right.  Most should work (Berensden should -- I think
Parrinello-Rahman currently doesn't, but the current NPT algorithm
should be used in place of Parrinello-Rahman for VV anyway).  And the
Nose-Hoover chains should be extended to leapfrog, though that should
be pretty easy once the variables are in the main structure.

> 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.

Sounds good.

I should have some more coding time starting Thursday for the next
couple weeks, so I'm happy to do whatever is needed.  I have a bunch
of free energy extensions I'd like to put in in the near future (i.e.,
this month, so my students can start a project) as well, so we should
discuss about putting it in my version, or waiting in the versions are

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

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