[gmx-users] shake for water

Tue Feb 10 08:10:44 CET 2009

> Date: Mon, 9 Feb 2009 12:00:52 -0600
> Subject: Re: [gmx-users] shake for water
> From: dmobley at gmail.com
> To: gmx-users at gromacs.org
> 
> > 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.
> 
> Er, yes, I have not turned on SHAKE -- I'm trying to use LINCS for
> bonds to hydrogen within my molecule and SETTLE for the waters. Sorry
> for the confusion in my original note.
> 
> Anyway -- any insights as to why I'd only be getting distances correct
> to 1e-6 with SETTLE?
> 
> Thanks,
> David
> 

Ah, now we are talking about something completely different.
Settle gets me at least 1e-10.
Are you sure your problem is in the water and not in the molecule with LINCS?
For LINCS you will need to change lincs_order to at least 8 and lincs_iter to something
probably something around 8.

Berk

> 
> >
> > 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
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
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