[gmx-users] CNT md simulation & unusual minimized structure

Atila Petrosian atila.petrosian at gmail.com
Thu Jul 19 13:08:26 CEST 2018

Dear gromacs users,

I am doing md simulation of cnt + drug (lig) + water molecules.

I get lig.gro and lig.itp files using antechamber module and amb2gmx script.

I used cnt force field parameters from paper

I get pdb file of cnt from nanotube modeller: (18,0), (Length = 34.468 Angstrom)

gmx_mpi editconf -f cnt.pdb -o cnt.gro -c -box 8 8 3.4468

gmx_mpi x2top -f cnt.gro -o cnt.top -ff cnt -name CNT -pbc -noparam

I merged gro files and itp and top files without problem.

gmx_mpi grompp -f em_vac.mdp -c complex.gro -p topol.top -o em_vac.tpr

gmx_mpi mdrun -v -deffnm em_vac -nb gpu >& em_vac.job &

gro file after energy minimization is unusual.


lig.itp, topol.top and cnt.ff is as follows, respectively:




Please guide me to resolve this problem.



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