[gmx-users] problem of pr.mdp file

[Mark Abraham]

sudheer wrote:
> hi gmx users
>  i have one doubt regarding pr.mdp file of protein.(my protein doesnt 
> contain any missing residues)
> This protein i have taken after run it in amber. The steps i have done are
> 1) pdb2gmx conversion
> 2) Energy minimisation in vaccum
>  Now my doubt is whats the next step ? directly i will go to production 
> or after doing postion restrain i have to do production?

It depends what you want to do the simulation for. See 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation for 
general advice, and consult the literature for how other people have 
done things similar to what you are doing.

Mark