[gmx-users] Errors in Minimization using grompp

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jun 13 10:53:19 CEST 2012

On 13/06/2012 6:44 PM, reisingere at rostlab.informatik.tu-muenchen.de 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.


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