[gmx-users] Ewald summation: segmentation fault!

[Alexandre Suman de Araujo]

Vincent Ballenegger wrote:

> Dear all,
> I'm having problems making the classical Ewald summation method work. 
> I find this strange because PME and PPPM work perfectly fine on the 
> other hand. When I set "coulombtype = Ewald", I get a segmentation 
> fault in mdrun. The last 3 lines in the md.log file are:
> acc: 0 0 0
> nfreeze: N N N
> energygrp_excl[ 0]: 0
>
> Gromacs (version 3.1.4) seems therefore to crash before reaching the 
> point where it should write:
> efield-x:
> n = 0
>
> in the .log file. My system is very simple: it consists in 2 ions in 
> an otherwise empty 3.5 nm box.
>
> File conf.gro:
> 2
> 1Na+ Na+ 1 2.691 2.691 0.809-39.2166-39.2166 39.2167
> 2Cl- Cl- 2 0.809 0.809 2.691 39.2166 39.2166-39.2167
> 3.50000 3.50000 3.50000
>
> where the Na+ and Cl- atoms are defined as
>
> [ atomtypes ]
> ;name mass charge ptype c6 c12
> Na+ 1.0 1.000 A 0.00000E+00 0.00000E+00
> Cl- 1.0 -1.000 A 0.00000E+00 0.00000E+00
>
> The (relevant parts of the) file generated by gromppp is
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing 
> electrostatics = coulombtype = Ewald
> rcoulomb-switch = 0
> rcoulomb = 0.9
> ; Dielectric constant (DC) for cut-off or DC of reaction field = 
> epsilon-r = 1
> ; Method for doing Van der Waals = vdw-type = Cut-off
> ; cut-off lengths = rvdw-switch = 0
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure = 
> DispCorr = No
> ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.6
> ; FFT grid size, when a value is 0 fourierspacing will be used = 
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters = pme_order = 4
> ewald_rtol = 1e-5
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
>
> ; Non-equilibrium MD stuff = acc-grps = accelerate = freezegrps = 
> freezedim = cos-acceleration = 0
>
> ; Electric fields = ; Format is number of terms (int) and for all 
> terms an amplitude (real) = ; and a phase angle (real) = E-x = 0
> E-xt = 0
> E-y = 0
> E-yt = 0
> E-z = 0
> E-zt = 0
>
> Thank you very much for helping me,
>
> Vincent Ballenegger
>
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>
I had the same problem and the same error in the same part of the .log 
file. I changed Ewald to PME and it worked. I thought it was a bug in 
GROMACS but I preferred to be quiet.
I hope constructive comments about this.

[]'s

-- 
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - Sa~o Carlos - Brasil