[gmx-users] shake for water

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 5 19:35:09 CET 2009

David Mobley wrote:
> All,
> A quick question on constraints... I'm using TIP4P-Ew in gromacs 3.3.2
> and am concerned with reproducing energies from another code very
> precisely for several specific snapshots. I am doing a zero-step mdrun
> of a setup with one small molecule and two tip4p-ew water molecules.
> Anyway, I have set the shake tolerance to 1e-12 in the mdp file, but
> to my surprise the internal water distances are good only to 1e-06 and
> 1e-07. Is this expected behavior? Note that I am running in double
> precision. I assumed that, er, the distances should converge to the
> shake tolerance.
Well, the documentation might be lacking, but the code tells the truth. 
It seems that the tolerance is used on the distance squared, which is 
consistent with your observation of a precision of 1e-6. So try 1e-24.

> Thanks,
> David
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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