[gmx-users] Ewald summation: n=0

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 23 09:19:21 CEST 2009

```Steve Fiedler wrote:
> Gromacs Users:
>
> While porting field parameters to Gromacs, I ran across unexpected
> electrostatic energies returned by the ewald summation method.  To
> simplify the problem, I reduced the system to two partially charged
> particles.  For the simplest case of only one box, n = 0, I expected to
> see contributions from the direct sum (Vdir) and self-interaction
> correction (V0) terms.  I can exactly match the analytical values for
> this system using DL_POLY, but the Gromacs Coulombic values obtained
> with gmx_dump appear to differ.  Most notably the presence of a
> canceling term (Vrec) was surprising in this case.
>
> To obtain n = 0, I set fourier_nx = fourier_ny = fourier_nz = 0, since m

These values override fourierspacing - zero just means not to override.
See various parts of section 7.3 of manual.

Mark

> = 2*pi*n/L^2 = 0. A subsequent gmx_dump yields:
> Coulomb (SR):  -10.4417 kJ/mol
> Coul. recip.  -63.6614 kJ/mol
> Coulomb + Coul. recip. = -74.2207 kJ/mol.
>
> My back of the envelope calculations are as follows:
> Beta = 3.47046 nm^-1 (from md.log)
> Vdir = -10.4416 kJ/mol, V0 = -2*43.5255 kJ/mol
> V = Vdir + V0 = -97.4927 kJ/mol.  Again, this matches the output from a
> DL_POLY calculation, but differs from the -74.2207 kJ/mol from above.
>
> As an experiment, I found a close, but inexact match to the analytical
> value by setting fourier_nx = fourier_ny = fourier_nz = 1. The below
> input files were used with Gromacs 4.0.4 in double precision.
> conf.gro
> -----------
> Two_Atoms
>  2
>    1DMP     AA    1   0.100   0.000   0.000
>    1DMP     BB    2   0.400   0.000   0.000
>  10.00000  10.00000  10.00000
>
> topol.top
> -----------
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1     2     no      0.125  1.0
>
> [ atomtypes ]
> ;name     mass     charge ptype  sig           eps
>   AA    10.0000   -0.400  A     0.39057      0.500
>   BB    10.0000    0.400  A     0.39057      0.700
> The below input files were used with Gromacs 4.0.4 in double precision.
> [ moleculetype ]
> TWOA 1
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>     1     AA    1      TWOA   AA      0       0.4000      10.0000
>     2     BB    1      TWOA   BB      0      -0.4000      10.0000
>
> [ system ]
> ; name
> Two atoms
>
> [ molecules ]
> ; name   number
> TWOA      1
>
> grompp.mdp
> -----------------
> integrator               = md
> dt                       = 0.002
> nsteps                   = 1
> ns_type                  = grid
> rlist                    = 0.9
> rcoulomb                 = 0.9
> rvdw                     = 0.9
> tcoupl                   = no
> pbc                      = xyz
> coulombtype              = Ewald
> ;fourierspacing           = 0
> ewald_rtol               = 1e-5
> fourier_nx                = 0
> fourier_ny                = 0
> fourier_nz                = 0
> pcoupl                   = no
>
>
> Thank you,
>
> Steve Fiedler
>
>
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