[gmx-developers] Re: Re: Re: Energy conservation
David van der Spoel
spoel at xray.bmc.uu.se
Mon Apr 10 19:25:15 CEST 2006
Erik Lindahl wrote:
> Hi Michael,
> On Apr 10, 2006, at 5:41 PM, Michael Shirts wrote:
>> 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?
> I'll see if I can find it, but don't hope too much since it was just a
> simple "playing" system with water - I might not have saved it.
> Anyway, the important parts are:
> 1. Use buffers in the neighborlist to account both for diffusion and
> finite charge group size.
> 2. Use switch, or PME with a significantly lower value of pme_rtol. I'm
> pretty sure the reciprocal part will conserve energy anyhow, so you
> don't need to worry about accuracy due to lower pme_rtol. Alternatively
> you can use your own tabulated function that is a switched-off ewald
> 3. Equilibrate well
> As I mentioned earlier today SETTLE conserves energy just fine - this
> was just a hack to be able to test LINCS using a tiny, well
> equilibrated, system instead of equilibrating a huge protein or something.
Just define -DFLEXIBLE in your mdp file and then constrain all-angles
>> 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.
> Check out the "test" module - there is some scattered stuff there. The
> primary regression tests are the benchmarks, our research runs of the
> day, and the kernel regression tests.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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