[gmx-users] simulation confined to a small region

[Filip Jagodzinski]

Has anybody had success on running 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