[gmx-users] Pull Peptide Apart

[Mark Abraham]

Joseph Johnson wrote:
> Hello All,
> 
> I'm fairly new to GROMACS so I apologize for if the question is simple.
> 
> I have a small peptide that I would like to pull apart.  What is the 
> process for doing this?  What type of things should I be reading into?  
> Is there any tutorials or code already for such a process?  I've seen 
> some things on freeze groups and accelerated groups and some on AFM 
> pulling but I'm confused as to where to start.

There's a bunch of tutorial material linked here 
http://wiki.gromacs.org/index.php/Category:Tutorials. You should get 
familiar with "normal" simulations before you make things complex by 
trying to pull apart your system. There's definitely a NAMD tutorial 
available for AFM pulling on their website, but the details will 
obviously be different.

Mark