[gmx-users] Why so many energy minimization and position restrained simulation steps?

[Mark Abraham]

Peggy Yao wrote:
> Hi,
> 
> I am new to Gromacs. I am following this tutorial:
> http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html. My
> question is: why it has multiple steps of energy minimization and
> position restrained simulation? Is that a common practice? What's the
> key difference among these steps?

There's some hints for general reasons for EM and PR here. 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

To find the particular reasons, look at the differences in the .mdp 
files using the Unix utility program "diff", and interpret in the 
context of GROMACS manual section 7.3.

Mark