[gmx-users] shake for water
Berk Hess
gmx3 at hotmail.com
Thu Feb 5 23:57:34 CET 2009
Hi David,
I just checked with shake tolerance 1e-10 I really get deviations of 1e-10.
First I forgot to turn on Shake and got the default Lincs,
which with the default settings gave me roughly the accuracy you reported.
(you did not by coincidence make the same mistake?)
Berk
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] shake for water
Date: Thu, 5 Feb 2009 23:02:31 +0100
Hi,
I don't agree.
It uses the small 1+a approximation for the square.
Also mdrun prints the rmsd determined with independent code,
which is consistent with the (correct) tolerance.
Berk
> Date: Thu, 5 Feb 2009 22:41:47 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] shake for water
>
> Berk Hess wrote:
> >
> >
> > > 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.
>
>
> First we compute the inverse square of the shake distance dA in tt[ll]
> for each shake pair:
>
> if (bFEP)
> toler = sqr(L1*ip[type].shake.dA + lambda*ip[type].shake.dB);
> else
> toler = sqr(ip[type].shake.dA);
> dist2[ll] = toler;
> tt[ll] = 1.0/(toler*tol2);
> }
>
> Then in the shake iteration we compute the difference between the
> squared distances (variable diff below):
>
> tx = xp[ix]-xp[jx];
> ty = xp[iy]-xp[jy];
> tz = xp[iz]-xp[jz];
> rpij2 = tx*tx+ty*ty+tz*tz;
> toler = dist2[ll];
> diff = toler-rpij2;
>
> Now we multiply the diff with tt[ll], in other words we get
> iconv = (1-rpij2/dist2)/(2 tol)
>
> /* iconv is zero when the error is smaller than a bound */
> iconv = fabs(diff)*tt[ll];
>
> In other words, the tolerance operates on the squared distance.
>
>
>
>
> >
> > 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?
> >
> > Berk
> >
> >
> > >
> > > >
> > > > 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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>
> --
> 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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