[gmx-users] shake for water
gmx3 at hotmail.com
Thu Feb 5 21:50:11 CET 2009
> Date: Thu, 5 Feb 2009 19:35:09 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] shake for water
> 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.
No, it is not the square.
The code does a small 'a' approximation: (1+a)^2=1+2a+a^2 is approx 1+2a.
I have also tested/benchmark shake in gromacs for my first lincs paper
and the plincs paper and it always behaved the way I thought it would.
The problem is not that you need more iterations than 1000?
And why not use settle that does it right at full precision at once?
> > 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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