[gmx-users] Ewald summation: segmentation fault!
Vincent Ballenegger
vcb25 at cam.ac.uk
Wed Apr 30 17:21:01 CEST 2003
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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