[gmx-users] shake for water

[David Mobley]

> 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?
>

Sorry, let me clarify. I was not that clear on the difference between
settle and shake. The issue is that I am using SETTLE to constrain the
water and I am only getting distances right to 1e-6 though I am
running in double precision.

David


> 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.
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