[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 
> interaction.
> 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 
using LINCS.

>> 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.
> Cheers,
> Erik
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-developers-request at gromacs.org.

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

More information about the gromacs.org_gmx-developers mailing list