[gmx-developers] energy conservation with constraints

Berk Hess hessb at mpip-mainz.mpg.de
Tue Apr 11 17:45:14 CEST 2006

Berk Hess wrote:

> Hi,
> I forgot two minus signs, inaccurate constraining should
> always decrease the energy. I have added sp shake.
> The energy drift over 100 ps as a fraction of Ekin is:
> dp, settle dp 0.0%
> sp, settle sp -0.6%
> sp, settle dp: -0.3%
> dp, settle dp, x rounded to sp at the beginning of each step: 0.0%
> dp, lincs dp order 8, iter 8: 0.0%
> dp, lincs dp order 8, iter 4: -0.3%
> sp, lincs sp order 8, iter 8: -2.1%
> sp, shake sp, tolerance 1e-5: +-0.3%
> sp, shake sp, tolerance 1e-4: -2.2%
I also found an old butane test system of 100 molecules.
The setup is roughly the same as for the water system.
dp, lincs dp order 8, iter 2: 0.0% over 400 ps
sp, lincs sp order8, iter 2: -0.3% over 100 ps
sp, shake sp 1e-5: -1.3% over 100 ps

The rigid water is a bad test case for lincs, as it has a very small
ring structure. Such structures never occur in non-angle constrained
With butane one can see that lincs provides good energy conservation.
As with settle one can probably only decrease the drift by storing
the whole state in double precision.


More information about the gromacs.org_gmx-developers mailing list