[gmx-users] grompp error (segmentation fault)in gromacs version 5.0.6

iamdsoumi iamdsoumi at gmail.com
Tue Aug 9 08:51:49 CEST 2016


    I carry on md run on protein-dna complex using  AMBER99SB-ILDN force
field. Here I state my problem.

       gmx_mpi pdb2gmx -f em267.pdb -o em267_processed.gro -p topol.top
-water tip3p -ignh
      it compile successfully.

          gmx_mpi editconf -f em267_processed.gro -o em267_newbox.gro -c -d
1.0 -bt cubic
        it compile successfully.

gmx_mpi solvate -cp newbox.gro -cs spc216.gro -p topol.top -o em267_solv.gro
it compile successfully.

gmx_mpi grompp -f em.mdp -c em267_solv.gro -p topol.top -o em267_ions.tpr

Here is the problem.

gromacs states

Ignoring obsolete mdp entry 'title'

NOTE 1 [file em.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 1779290498

WARNING 1 [file topol_DNA_chain_D.itp, line 5]:
  Too few gb parameters for type localhost.localdomain

Couldn't find topology match for atomtype localhost.localdomain
Segmentation fault (core dumped)

I always take back up of the trajectory file in my external hard disk and
delete the data from gpu.

What is the problem ?Problem even exists in  pdb which can be run foremerly
without any problem.Does anyone know how to solve this issue?


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