On 13/06/2012 6:44 PM, [email protected] wrote:
Hi everybody,
I want to do a minimization of the hydrogens of my protein. Only the
hydrogens.
Doesn't really matter - nothing will move more than a fraction of an
Angstrom unless it's horribly wrong, in which case not moving the heavy
atoms won't help you.
And I want to do this with implicit solvent.
Probably not worth the effort if you're just preparing for MD.
All the time when I try it there are errors in my .mdp file. Can you
please give me an example how such a .mdp file should look like.
Every tutorial you've done will have an example EM .mdp file. Searching
Google for some implicit solvent examples will provide some leads.
Ultimately you need to learn how to create and manage one, so hoping one
will appear and using it blindly is not terribly productive.
Mark
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