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

soumi soumi90 at rediffmail.com
Fri Aug 5 09:59:58 CEST 2016

Hi,    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.groit compile successfully.gmx_mpi grompp -f em.mdp -c em267_solv.gro -p topol.top -o em267_ions.tprHere is the problem.gromacs statesIgnoring 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 17792
 90498WARNING 1 [file topol_DNA_chain_D.itp, line 5]:  Too few gb parameters for type localhost.localdomainCouldn't find topology match for atomtype localhost.localdomainSegmentation 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?Thanks.Soumi

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