[gmx-users] RE: mdp files

[Vitaly Chaban]

> Special thanks to Vitaly, Mark and Justin for there comments. I've
> revisited the wiki site and read through chapter 5 of the manual. I'm
> currently going through the tutorial with a standard protein. I run into a
> problem when I use the command:
> 
> grompp -f em.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr
> 
> The error states that the em.mdp file doesn't exists, but none of the
> steps in the tutorial leading up to this command creates the em.mdp file.
> I was just wondering what step in the process is the .mdp file created or
> do I have to have that already created off to the side ready for the
> grompp command?
> 
> Thanks again,
> 
> -John Landers

I guess em.mdp is a parameter file for energy minimization. Look here:
http://www.gromacs.org/documentation/reference/online/mdp.html for how
one can make it. If you want to make an energy minimization of your
system firstly, you just have to change
"integrator = md"
to
"integrator = l_bfgs"
or
"integrator = steep"

I have also sent you personally the ready example to start with
simulating carbon nanotube.

Best,
Vitaly