[gmx-users] Grompp Error : Segmentation fault

Roland Schulz roland at utk.edu
Tue Sep 28 18:15:12 CEST 2010


Please make sure that the error exists in the latest version. Either 4.5.1
or if you know how please check the latest GIT version
from release-4-5-patches. If you still get the error with the latest
version, please file a bugzilla report and attach all required files.

On Tue, Sep 28, 2010 at 9:01 AM, Alep Latep <m.alif.m.latif at gmail.com>wrote:

> 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-
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100928/0569e99c/attachment.html>


More information about the gromacs.org_gmx-users mailing list