README for Born APBS examples

This is the canonical electrostatics test case: Born ion. A non-polarizable ion with a single embedded point charge; has an analytical solution for the potential. We examine the solvation free energy as a function of ionic radius.

Please see apbs.in for details on the particular solvation energy calculations. Analytical results are given in pmf.dat.

This example was contributed by Nathan Baker.

Input File	Description	APBS Version	Results (kJ/mol)	Analytical (kJ/mol)
apbs-mol-auto.in	Sequential, 3 A sphere, 3-level focusing to 0.188 A, srfm mol	1.4.2	-229.774	-230.62
		1.4.1	-229.7736
		1.4	-229.7736³
		1.3	-229.7735
		1.2.1	-229.7735
		1.2	-229.7735
		1.1.0	-229.7735
		1.0.0	-229.7735
		0.5.1	-229.7735
		0.5.0	-229.7735
		0.4.0	-229.7735¹
		0.3.2	-229.7248
		0.3.1	-229.7248
		0.3.0	-229.7248
		0.2.6	-229.7248
		0.2.5	-229.7248
		0.2.4	-227.1859
		0.2.3	-227.1589
		0.2.2	-227.186
		0.2.1	-227.19
		0.2.0	-227.19
		0.1.8	-227.19
apbs-smol-auto.in	Sequential, 3 A sphere, 3-level focusing to 0.188 A, srfm smol	1.4.2	-229.012	-230.62
		1.4.1	-229.0124
		1.4	-229.0124
		1.3	-229.0124
		1.2.1	-229.0124
		1.2	-229.0124²
		1.1.0	-229.0123
		1.0.0	-229.0123
		0.5.1	-229.0123
		0.5.0	-229.0123
		0.4.0	-229.0123
apbs-mol-parallel.in	Parallel with 4 processors, 3 A sphere, focusing to 0.103 A, srfm mol	1.4.2	-230.492	-230.62
		1.4.1	-230.4918⁴
		1.4	-230.4919³
		1.3	-230.4918
		1.2.1	-230.4918
		1.2	-230.4918²
		1.1.0	-230.4916
		1.0.0	-230.4916
		0.5.1	-230.4916
		0.5.0	-230.4916
		0.4.0	-230.4916
		0.2.1	-230.77
apbs-smol-parallel.in	Parallel with 4 processors, 3 A sphere, focusing to 0.103 A, srfm smol	1.4.2	-229.387	-230.62
		1.4.1	-229.3871
		1.4	-229.3871
		1.3	-229.3871
		1.2.1	-229.3871
		1.2	-229.3871²
		1.1.0	-229.3872
		1.0.0	-229.3872
		0.5.1	-229.3872
		0.5.0	-229.3872
		0.4.0	-229.3872¹
		0.3.2	-226.3529
		0.3.1	-226.3529
		0.3.0	-229.5849
		0.2.6	-229.5849
		0.2.5	-229.5849
		0.2.4	-226.2276
		0.2.3	-226.2276
		0.2.2	-226.2276
		0.2.0	-226.228
		0.1.8	-226.23
apbs-smol-parallel.in	Finite Element Method, 3 A sphere, 3-level focusing to 0.188 A, srfm mol	1.4.1-binary	-231.9550	-230.62
apbs-smol-parallel.in	Finite Element Method, 3 A sphere, 3-level focusing to 0.188 A, srfm smol	1.4.1-binary	-230.9760	-230.62

¹ The discrepancy in values between versions 0.4.0 and 0.3.2 is most likely due to three factors:

A bug fix in Vacc_molAcc which removed spurious regions of high internal dielectric values
A switch in the algorithm used to compute the dielectric smoothing for srfm smol.
The addition of the Vacc sphere density (sdens keyword) as a variable and a change in the default sdens value from 3.0 to 10.0

² APBS 1.2 has switched the multigrid smoothing algorithm from standard Gauss-Seidel to Gauss-Seidel red/black in order to facilitate parallelization. This switch has caused small differences in individual calculation energies which, when combined to the final answer, create larger errors (up to 0.04%). These errors can be reduced by resetting the APBS error tolerance to 1e-9 or smaller values. For a more detailed explanation, please see the APBS FAQ, [here](http://www.poissonboltzmann.org/docs/apbs-faq/#sources error calculation).

³ The discrepancy in values between versions 1.3 and 1.4 is most likely due to the following factor(s):

Translation of contrib/pmgZ library from FORTRAN to C
Differences in numerical implementations between FORTRAN and C compilers result in small round-off discrepencies
Small margins due to these round-off discrepencies acumulate in the computations

⁴ The discrepancy in the result between versions 1.4 and 1.4.1-binary is most likely due to a reporting error.

Please see the ChangeLog or the APBS website for more information.

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README for Born APBS examples

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