[gmx-users] simulation confied to a small region

[Filip Jagodzinski]

I would like to run a simulation on only a part of a protein. I have a 
very large protein, and I'm only concerned with analyzing the motions of 
two specific close sidechains rather than analyzing the complete system. 
Do you recommend that I set the simulation box to very very small 
dimensions and then orient the box so that the two side chains are in the 
center of the box? If that's how it is done, I've had no luck with using 
editconf. Any suggestions?

Much thanks