[gmx-users] Problem setting up SMD simulation for DNA

[Nicholus Bhattacharjee]

Hello user,

I am trying to setup SMD simulation for a DNA. I am following the tutorial
from Bevanlab where SMD was on protein performed to use as input for
umbrella sampling.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

Now for initial setup I am using the following command

$ gmx_mpi pdb2gmx -f start.pdb -ignh -ter -o dna.gro

I am getting new files posre.itp, topol.top & dna.gro

According to the tutorial I should also get another file like topol_***.itp
whi I need to modify for SMD simulation. Kindly let me know if I am doing
anything wrong.

Thank you in advance for the help.

regards