[gmx-users] Grompp Error : Segmentation fault

Alep Latep m.alif.m.latif at gmail.com
Tue Sep 28 15:01:07 CEST 2010


Dear Gromacs Users and Developers,

I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic
liquid MD simulation using amber 99 force field. I got my topology from
topolbuild v 1.3. I successfully minimized both cation and anion separately
using cg and steep. Then I include the anion in the cation system using
genbox. I got error from grompp like this:
------------------------------------------------------------------------------
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
processing topology...
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Segmentation fault (core dumped)
[alif at NeoX MD1]$
---------------------------------------------------------------------------------
Still cant find my answer in the mailing list. Sorry for the large post, but
here's my .mdp and .top

---------------------------------------------------------------------------------
title = Conjugated-Gradients Energy Minimization

; Preprocessing
cpp = /lib/cpp
include = -I../top

; Parameters
integrator = cg
emtol = 1.0
nsteps = 5000
nstenergy = 100
nstxtcout = 100
xtc_grps = System
energygrps = System

; Neighboursearching
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
constraints = none
pbc = xyz
-----------------------------------------------------------------------------------------------------
; Topology from .mol2 file
; topolbuild version 1.3
; Command line:
;     topolbuild -n BMIM_Test3 -ff amber99 -dir $AMBERHOME
;
; The force field files to be included
#include "amber99.ff/forcefield.itp"

 [ moleculetype ]
; name  nrexcl
BMIM   3

 [ atoms ]
;  nr    type   resnr   residu   atom   cgnr    charge      mass
    1          CT     1      BMIM       C    1  -0.17243  12.01100       ;
 -0.1724300
    2          HC     1      BMIM       H    1   0.07139   1.00800       ;
 -0.1010400
    3          HC     1      BMIM       H    1   0.05434   1.00800       ;
 -0.0467000
    4          HC     1      BMIM       H    1   0.05138   1.00800       ;
0.0046800
    5          CT     1      BMIM       C    2   0.02353  12.01100       ;
0.0282100
    6          HC     1      BMIM       H    2   0.02417   1.00800       ;
0.0523800
    7          HC     1      BMIM       H    2   0.02427   1.00800       ;
0.0766500
    8          CT     1      BMIM       C    3   0.01014  12.01100       ;
0.0867900
    9          HC     1      BMIM       H    3   0.03312   1.00800       ;
0.1199100
   10          HC     1      BMIM       H    3   0.02952   1.00800       ;
0.1494300
   11          NA     1      BMIM       N    4   0.05435  14.00670       ;
0.2037800
   12          CC     1      BMIM       C    4  -0.17380  12.01100       ;
0.0299800
   13          H4     1      BMIM       H    4   0.23709   1.00800       ;
0.2670700
   14          NA     1      BMIM       N    6   0.07275  14.00670       ;
0.3398200
   15          CT     1      BMIM       C    5  -0.07367  12.01100       ;
0.2661500
   16          H1     1      BMIM       H    5   0.10657   1.00800       ;
0.3727200
   17          H1     1      BMIM       H    5   0.09108   1.00800       ;
0.4638000
   18          CC     1      BMIM       C    6  -0.08433  12.01100       ;
0.3794700
   19          H4     1      BMIM       H    6   0.20500   1.00800       ;
0.5844700
   20          CR     1      BMIM       C    7  -0.02624  12.01100       ;
0.5582300
   21          H5     1      BMIM       H    7   0.21862   1.00800       ;
0.7768500
   22          CT     1      BMIM       C    8  -0.18403  12.01100       ;
0.5928200
   23          H1     1      BMIM       H    8   0.13823   1.00800       ;
0.7310500
   24          H1     1      BMIM       H    8   0.13886   1.00800       ;
0.8699100
   25          H1     1      BMIM       H    8   0.13010   1.00800       ;
1.0000100
; total molecule charge =   1.0000100

 [ bonds ]
;   ai  aj   funct      b0          kb
       1     5   1     0.15260      259408.       ;     C-     C
       1     2   1     0.10900      284512.       ;     C-     H
       1     3   1     0.10900      284512.       ;     C-     H
       1     4   1     0.10900      284512.       ;     C-     H
       5     8   1     0.15260      259408.       ;     C-     C
       5     6   1     0.10900      284511.       ;     C-     H
       5     7   1     0.10900      284512.       ;     C-     H
       8    15   1     0.15260      259408.       ;     C-     C
       8     9   1     0.10900      284512.       ;     C-     H
       8    10   1     0.10900      284512.       ;     C-     H
      11    12   1     0.13850      353129.       ;     N-     C
      11    15   1     0.13850      353129.       ;     N-     C
      11    20   1     0.13850      353129.       ;     N-     C
      12    18   1     0.14000      392459.       ;     C-     C
      12    13   1     0.10800      307106.       ;     C-     H
      14    18   1     0.13850      353129.       ;     N-     C
      14    20   1     0.13850      353129.       ;     N-     C
      14    22   1     0.13850      353129.       ;     N-     C
      15    16   1     0.10900      284512.       ;     C-     H
      15    17   1     0.10900      284512.       ;     C-     H
      18    19   1     0.10800      307106.       ;     C-     H
      20    21   1     0.10800      307106.       ;     C-     H
      22    23   1     0.10900      284512.       ;     C-     H
      22    24   1     0.10900      284512.       ;     C-     H
      22    25   1     0.10900      284512.       ;     C-     H

 [ pairs ]
       2       8  1       ;     H-     C
       2       6  1       ;     H-     H
       2       7  1       ;     H-     H
       3       8  1       ;     H-     C
       3       6  1       ;     H-     H
       3       7  1       ;     H-     H
       4       8  1       ;     H-     C
       4       6  1       ;     H-     H
       4       7  1       ;     H-     H
       1      15  1       ;     C-     C
       1       9  1       ;     C-     H
       1      10  1       ;     C-     H
       6      15  1       ;     H-     C
       6       9  1       ;     H-     H
       6      10  1       ;     H-     H
       7      15  1       ;     H-     C
       7       9  1       ;     H-     H
       7      10  1       ;     H-     H
       5      11  1       ;     C-     N
       5      16  1       ;     C-     H
       5      17  1       ;     C-     H
       9      11  1       ;     H-     N
       9      16  1       ;     H-     H
       9      17  1       ;     H-     H
      10      11  1       ;     H-     N
      10      16  1       ;     H-     H
      10      17  1       ;     H-     H
      15      18  1       ;     C-     C
      15      13  1       ;     C-     H
      20      13  1       ;     C-     H
      12       8  1       ;     C-     C
      12      16  1       ;     C-     H
      12      17  1       ;     C-     H
      20       8  1       ;     C-     C
      20      16  1       ;     C-     H
      20      17  1       ;     C-     H
      12      21  1       ;     C-     H
      15      14  1       ;     C-     N
      15      21  1       ;     C-     H
      11      19  1       ;     N-     H
      13      14  1       ;     H-     N
      13      19  1       ;     H-     H
      20      19  1       ;     C-     H
      22      12  1       ;     C-     C
      22      19  1       ;     C-     H
      18      21  1       ;     C-     H
      22      11  1       ;     C-     N
      22      21  1       ;     C-     H
      18      23  1       ;     C-     H
      18      24  1       ;     C-     H
      18      25  1       ;     C-     H
      20      23  1       ;     C-     H
      20      24  1       ;     C-     H
      20      25  1       ;     C-     H

[ angles ]
; ai  aj  ak  funct      th0         cth
     2     1     5   1     109.500    418.4000     ;     H-     C-     C
     3     1     5   1     109.500    418.4000     ;     H-     C-     C
     4     1     5   1     109.500    418.4000     ;     H-     C-     C
     1     5     8   1     109.500    334.7200     ;     C-     C-     C
     1     5     6   1     109.500    418.4000     ;     C-     C-     H
     1     5     7   1     109.500    418.4000     ;     C-     C-     H
     3     1     2   1     109.500    292.8800     ;     H-     C-     H
     4     1     2   1     109.500    292.8800     ;     H-     C-     H
     4     1     3   1     109.500    292.8800     ;     H-     C-     H
     6     5     8   1     109.500    418.4000     ;     H-     C-     C
     7     5     8   1     109.500    418.4000     ;     H-     C-     C
     5     8    15   1     109.500    334.7200     ;     C-     C-     C
     5     8     9   1     109.500    418.4000     ;     C-     C-     H
     5     8    10   1     109.500    418.4000     ;     C-     C-     H
     7     5     6   1     109.500    292.8800     ;     H-     C-     H
     9     8    15   1     109.500    418.4000     ;     H-     C-     C
    10     8    15   1     109.500    418.4000     ;     H-     C-     C
     8    15    11   1     109.500    418.4000     ;     C-     C-     N
     8    15    16   1     109.500    418.4000     ;     C-     C-     H
     8    15    17   1     109.500    418.4000     ;     C-     C-     H
    10     8     9   1     109.500    292.8800     ;     H-     C-     H
    15    11    12   1     126.400    585.7600     ;     C-     N-     C
    20    11    12   1     120.000    585.7600     ;     C-     N-     C
    11    12    18   1     126.400    585.7600     ;     N-     C-     C
    11    12    13   1     120.000    418.4000     ;     N-     C-     H
    20    11    15   1     126.400    585.7600     ;     C-     N-     C
    11    15    16   1     109.500    418.4000     ;     N-     C-     H
    11    15    17   1     109.500    418.4000     ;     N-     C-     H
    11    20    14   1     120.000    585.7600     ;     N-     C-     N
    11    20    21   1     120.000    418.4000     ;     N-     C-     H
    13    12    18   1     120.000    418.4000     ;     H-     C-     C
    12    18    14   1     126.400    585.7600     ;     C-     C-     N
    12    18    19   1     120.000    418.4000     ;     C-     C-     H
    20    14    18   1     120.000    585.7600     ;     C-     N-     C
    22    14    18   1     126.400    585.7600     ;     C-     N-     C
    14    18    19   1     120.000    418.4000     ;     N-     C-     H
    22    14    20   1     120.000    585.7600     ;     C-     N-     C
    14    20    21   1     120.000    418.4000     ;     N-     C-     H
    14    22    23   1     109.500    418.4000     ;     N-     C-     H
    14    22    24   1     109.500    418.4000     ;     N-     C-     H
    14    22    25   1     109.500    418.4000     ;     N-     C-     H
    17    15    16   1     109.500    292.8800     ;     H-     C-     H
    24    22    23   1     109.500    292.8800     ;     H-     C-     H
    25    22    23   1     109.500    292.8800     ;     H-     C-     H
    25    22    24   1     109.500    292.8800     ;     H-     C-     H

[ dihedrals ]
; ai  aj   ak  al          funct    phi0          cp      mult
     2     1     5     8   1       0.000       0.669         3  ; dih
 H-     C-     C-     C
     1     5     8    15   1       0.000       0.753         3  ; dih
 C-     C-     C-     C
     1     5     8    15   1     180.000       1.046         2  ; dih
 C-     C-     C-     C
     1     5     8    15   1     180.000       0.837         1  ; dih
 C-     C-     C-     C
     5     8    15    11   1       0.000       0.651         3  ; dih
 C-     C-     C-     N
    20    11    12    18   9     180.0       5.85760         2  ; dih
 C-     N-     C-     C
    12    11    15     8   1       0.000       0.000         2  ; dih
 C-     N-     C-     C
    12    11    20    14   9     180.0       5.85760         2  ; dih
 C-     N-     C-     N
    11    12    18    14   1     180.000      15.167         2  ; dih
 N-     C-     C-     N
    20    14    18    12   9     180.0       5.85760         2  ; dih
 C-     N-     C-     C
    18    14    20    11   9     180.0       5.85760         2  ; dih
 C-     N-     C-     N
    18    14    22    23   1       0.000       0.000         2  ; dih
 C-     N-     C-     H
    11    12    15    20   1     180.000       4.602         2  ; imp
 N-     C-     C-     C
    12    11    18    13   1     180.000       4.602         2  ; imp
 C-     N-     C-     H
    14    18    20    22   1     180.000       4.602         2  ; imp
 N-     C-     C-     C
    18    12    14    19   1     180.000       4.602         2  ; imp
 C-     C-     N-     H
    20    11    14    21   1     180.000       4.602         2  ; imp
 C-     N-     N-     H

; Include Position restraint file
; WARNING: Position restraints and distance restraints ought not be done
together
#ifdef POSRES
#include "posreBMIM_Test3.itp"
#endif

; Include TFO topology
#include TFO_amber99.itp

; Include water topology
#include "tip3p.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 ]
; title from mol2 input
BMIMTFO

 [ molecules ]
; molecule name    nr.
BMIM           1
TFO 1
--------------------------------------------------------------------------------------------
Any thought, advice and support is greatly appreciated. Thank you.

-Alif-
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