[gmx-users] .mdp files

[Erik Lindahl]

subramaniam sivaraman wrote:
> Hi,
>   If I am interested in running the preprocessor
> grompp, is it necessary for us to supply the
> grompp.mdp file for that( since it is input, opt) and
> I would like to know whether the grompp.mdp file can
> be used along with any protein of our interest. Is it
> the correct way to give grompp.mdp as input file and
> generate for eg. x.mdp of our interest. Advance thanks
> for the help. Also, please suggest how to generate the
> full.mdp for the proteins of our interest.
>                              s.sivaraman
> 

The *.mdp file (it can have any name you want, grompp.mdp is just the 
default) contains all your options, like the number of steps, how
often you want to write data, electrostatics methods, etc. The only
way it is "optional" is that grompp will use default values for options
you don't include, so if you don't provide the file every single option
will have its default value. You probably don't want that :-)

Cheers,

Erik