[gmx-users] shake for water

[David Mobley]

> 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


>
> 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
>> > > > _______________________________________________
>> > > > gmx-users mailing list gmx-users at gromacs.org
>> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > > > Please search the archive at http://www.gromacs.org/search before
>> > posting!
>> > > > Please don't post (un)subscribe requests to the list. Use the
>> > > > www interface or send it to gmx-users-request at gromacs.org.
>> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> > >
>> > >
>> > > --
>> > > 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
>> > > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > > Please search the archive at http://www.gromacs.org/search before
>> > posting!
>> > > Please don't post (un)subscribe requests to the list. Use the
>> > > www interface or send it to gmx-users-request at gromacs.org.
>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >
>> > ------------------------------------------------------------------------
>> > Express yourself instantly with MSN Messenger! MSN Messenger
>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
>> >
>> >
>> > ------------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > gmx-users mailing list gmx-users at gromacs.org
>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at http://www.gromacs.org/search before
>> > posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>> --
>> 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
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> ________________________________
> Express yourself instantly with MSN Messenger! MSN Messenger
> ________________________________
> See all the ways you can stay connected to friends and family
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>