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

[Atila Petrosian]

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
(*https://pubs.acs.org/doi/abs/10.1021/jp011344u
<https://pubs.acs.org/doi/abs/10.1021/jp011344u>*)



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.



https://1drv.ms/u/s!AveJH4Y30cH0sQnyV-5RoaqhaeFJ





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



https://1drv.ms/u/s!AveJH4Y30cH0sHioMbu0GT2BDATg



https://1drv.ms/u/s!AveJH4Y30cH0sHrSTs-0f0kK-mE5



https://1drv.ms/f/s!AveJH4Y30cH0rEU08meMh0EEfQde





Please guide me to resolve this problem.


Best,

Atila