[gmx-users] segmentation fault with mdrun
jalemkul at vt.edu
Tue Aug 21 12:05:11 CEST 2012
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:
> 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
> ; 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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