[gmx-users] shake for water
David van der Spoel
spoel at xray.bmc.uu.se
Tue Feb 10 18:54:44 CET 2009
David Mobley wrote:
> Berk,
>> 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.
>
> I am using trjconv with -ndec to output the coordinates to gro files
> to 12 decimal places, then computing the distances between the atoms
> in the water from these coordinates. So yes, I am sure I am looking at
> the water molecules. The distances in question are only right to
> ~1e-6.
>
> Should I send input files?
Of course you are welcome to send a bugzilla.
You can also use g_bond to plot a bond histogram of water.
(g_bond -blen 0.1 -tol 1e-5 or something along those lines)
>
> Thanks,
> David
>
>
>> 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
>>>>>>> _______________________________________________
>>>>>>> gmx-users mailing list gmx-users at gromacs.org
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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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--
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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