[gmx-users] segmentation fault with mdrun

[Justin Lemkul]

On 8/21/12 6:00 AM, Deepak Ojha wrote:
> 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.
>

Don't use -maxwarn unless you know exactly why you're doing it.  The fact that 
you have 327 non-matching names and 327 atoms in the system (108*3 + 3) suggests 
the contents of your coordinate file do not match that of the topology in terms 
of the order of the [molecules] section.  Likely your azide should be listed 
first, presumably if you took the coordinate file for this molecule and solvated it.

Also beware that PRODRG topologies are notoriously unreliable and that linear 
molecules should not be constructed in this way (180 degree angles are not 
stable).  See, for instance, the following tutorial for a more robust method:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html

-Justin

>
> 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"
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================