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
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