[gmx-users] segmentation fault with mdrun

[Deepak Ojha]

Dear All
I am trying to perform the  azide ion in water simulation with
Gromacs. I generated to topology file with PRODG server for azide ion
and ran the calculations.I got one error at grompp  level which was  "

  327 non-matching atom names
  atom names from azide.top will be used
  atom names from azide.gro will be ignored

I continued with the maxwarn and performed energy minimization which
went smoothly.However no sooner I started equilibration in NVT run
using mdrun
it crashed with segmentation fault. Please help me to locate the
error. I went through the previous mails on the mailing list but I
could not sort it out.


The topology file is :

; Include forcefield parameters
#include "ffG43a1.itp"

;Include azide topology
#include "azide.itp"

; Include water topology
#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
azide in water

[ molecules ]
; Compound        #mols
SOL               108
AZI               1


and the itp file for azide which I made from PRODG is

[ moleculetype ]
; Name nrexcl
AZI      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1         N     1  AZI      N1     1   -1.000  14.0067
     2         N     1  AZI      N2     1    2.000  14.0067
     3         N     1  AZI      N3     1   -1.000  14.0067

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.112   4527362.4    0.112   4527362.4 ;    N2   N1
   2   3   2    0.112   4527362.4    0.112   4527362.4 ;    N2   N3

[ pairs ]
; ai  aj  fu    c0, c1, ...

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    180.0  41840001.2    180.0  41840001.2 ;    N1   N2   N3

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...

--

DeepaK Ojha
School Of Chemistry

"Selfishness is not living as one wishes to live, it is asking others
to live as one wishes to live"