[gmx-developers] Re: re: Velocity verlet version of Gromacs with trotter-decomposition NPT (Berk Hess)
mrshirts at gmail.com
Tue Oct 13 15:00:37 CEST 2009
> 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.
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.
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
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
More information about the gromacs.org_gmx-developers