[gmx-users] Re: ewald_rtol and convergence

[David van der Spoel]

Michael Shirts wrote:
> So, it turns out that the problem with the poor convergence is that I
> accidentally had pbc = no set instead of pbx = xyz in the mdp.  Once
> that was fixed, covergence was much more reasonable.
> 
> I'm wondering if there should be a warning in the code that says "Do
> you REALLY want to use Ewald with a non-periodic system?"
> 
Done.

> Thanks,
> Michael
> 
> On 2/17/06, Michael Shirts <mrshirts at gmail.com> wrote:
> 
>>Hi, all-
>>
>>So, I'm wondering what the effect of ewald_rtol is.  My understanding
>>is that it should just be shifting the calculation between the real
>>space and the reciprocal space summations.  But the total
>>electrostatic is changing non-negligibly as well.  My system is a box
>>of waters with a protein -- total charge is zero.  PME Cutoff is 0.9,
>>fourier_spacing is 0.02 (so well converged in all cases), PME order 6.
>>Octahedral box, (5.78643,5.45550,4.72461) box vector, all the same
>>configuration.
>>
>>Ewald_rtol                   total                  Short range
>> Long range         1/beta (nm)
>>1e-02                  -53195.725708   -46946.948640     -6248.777068
>>     0.494129
>>1e-03                  -53432.220675   -45014.961538     -8417.259138
>>     0.386805
>>1e-04                  -53652.773007   -43093.541701   -10559.231306
>>    0.327146
>>1e-05                  -53872.777698   -41119.255332   -12753.522366
>>    0.288146
>>1e-06                  -54092.976378   -39070.390423   -15022.585955
>>    0.260198
>>
>>I did some comparison to straight Ewald, as well.
>>
>>Ewald_rtol                   total                  Short range
>> Long range
>>1e-02                   -52899.579997   -46946.948640    -5952.631357
>>1e-03                   -53001.090875   -45014.961538    -7986.129337
>>1e-05                   -53182.993892   -41119.255332   -12063.738560
>>
>>We see that the short range part is exactly the same in PME and
>>straight Ewald, as it should, though the long range part is not the
>>same, even when the PME part is well converged (i.e., I reduced the
>>fourier_spacing until any changes were sub 0.002 kJ/mol, which is one
>>part in 25 million).
>>
>>I'm unsure why the differences.  It there coding issue with the
>>octahedral box? Is there some effect with the dielectic at infinity
>>(i'm using epsilon_surface = 0).  What is the 'true' electrostatic
>>energy?
>>I tried different cutoffs -- presumably, as we take a low rtol,
>>pushing the calculation further into the direct space, and choose a
>>longer cutoff, the correction will get more accurate.
>>
>>PME: (order 6, ewald_rtol = 1e-02)
>>cutoff                     total                  Short range
>>Long range             1/beta
>>
>>0.9                  -53195.725708   -46946.948640     -6248.777068
>>   0.494129
>>1.8                  -52875.688467   -49910.307947     -2965.380520
>>   0.988258
>>2.7                  -52798.032604   -50836.767614     -1961.264991
>>   1.48239
>>3.6                  -52764.124490   -51296.887618     -1467.236872
>>   1.97652
>>4.5                  -52745.340510   -51572.825196     -1172.515314
>>   2.47065
>>
>>Ewald: (fourier_nx,ny,nz = 25)
>>
>>0.9                  -52899.579997   -46946.948640    -5952.631357
>>    0.494129
>>1.8                  -52785.799065   -49910.307947    -2875.491118
>>    0.988258
>>2.7                  -52761.626727   -50836.767614    -1924.859113
>>    1.48239
>>3.6                  -52747.927053   -51296.887618    -1451.039435
>>    1.97652
>>4.5                  -52738.223387   -51572.825196    -1165.398191
>>    2.47065
>>
>>So it seems that -52730 is closer to the "right" answer.  Why isn't
>>this more possible to with other combinations of terms?  Am I missing
>>something?  Is this level of agreement (both for Ewald, and between
>>PME and Ewald) an unreasonable expectation? :)
>>
>>Thanks,
>>Michael
>>
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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