[gmx-users] Anisotropic system with coulomb(PME) + Buckinghum

[hiroo_fukunaga at fujifilm.co.jp]

Hello gmx-users,

I try MD simulation for an anisotropic inorganic system(a=b.ne.c;
alpha=beta=90, gamma=120).
The system contains only coulomb interaction and Buckinghum potentials
I made .top file myself.
The coloumb interaction is calculated using PME algorithm.
 I took coordinates from the x-ray structure to make .gro file.

My .top file is as follows.
[ defaults ]
; non-bond type  combination rule
2 1
[ atomtypes ]
;name        mass      charge   ptype       A            B         C6
 OBKS    15.99940        0.0        A      0.0          0.0       0.0
SIBKS    28.08000        0.0        A      0.0          0.0       0.0
[ nonbond_params ]
  ; i    j func           a             b       c6
 OBKS  OBKS    2 1.339973E+5          27.6       1.688480E-2
SIBKS  OBKS    2 1.737084E+6       48.7318       1.288436E-2
SIBKS SIBKS    2         0.0           0.0       0.0
[ moleculetype ]
; name nrexcl
SIBKS     0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1     SIBKS     1     SIBKS    SIBKS    1       2.4     28.08000
[ moleculetype ]
; name nrexcl
OBKS     0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1      OBKS     1      OBKS     OBKS    2       -1.2    15.99940
[ system ]
; Name
Silica SiO2
[ molecules ]
; Compound    #mols
SIBKS        192
OBKS         384


My .mdp file is as follows.

title               =  Yo                 ; a string
cpp                 =  cpp                ; c-preprocessor
dt                  =  0.001              ; time step
nsteps              =  1000               ; number of steps
nstcomm             =  1                  ; reset c.o.m. motion
nstxout             =  500                ; write coords
nstvout             =  10000              ; write velocities
nstlog                =  50               ; print to logfile
nstenergy           =  50                 ; print energies
nstlist             =  10                 ; update pairlist
ns_type             =  simple             ; pairlist method
vdw-type            = Shift
rvdw-switch         = 0.7
coulombtype         =  PME                ; coulomb type
rcoulomb-switch      = 0
ewald_rtol          =  1e-5
ewald_geometry      = 3d
fourierspacing      =  0.1
fourier_nx          = 0
fourier_ny          = 0
fourier_nz          = 0
pme_order           =  4
rlist               =  0.8                ; cut-off for ns
rvdw                =  0.8                ; cut-off for vdw
rcoulomb            =  0.8                ; cut-off for coulomb
Tcoupl              =  nose-hoover          ; temperature coupling
ref_t           =  10
tc-grps               =  System
tau_t           =  0.1
Pcoupl              =  Parrinello-Rahman         ; pressure bath
Pcoupltype          =  anisotropic        ; pressure geometry
tau_p               =  1                  ; p-coupoling time
compressibility     =  4.5e-5 4.5e-5      4.5e-5      4.5e-5      4.5e-5
4.5e-5
ref_p               =  1.0 1.0 1.0 1.0 1.0 1.0
gen_vel             =  yes                ; generate initial velocities
gen_temp            =  10                 ; initial temperature
gen_seed            =  1993               ; random seed
epsilon-r           = 1
epsilon_surface     = 0
optimize_fft        = yes


As a result of mdrun, I got an error message.

step 0 Segmentation fault(core dumped)

Please help me.

Hiroo Fukunaga


*********************************************
Hiroo Fukunaga

FUJI PHOTO FILM CO., LTD.
Ashigara Research Laboratories
210, Nakanuma, Minamiashigara-shi, Kanagawa, 250-0193, Japan
TEL 81-465-73-7056 FAX 81-465-73-7935
E-mail hiroo_fukunaga at fujifilm.co.jp
*********************************************