[gmx-users] MD on part of protein

[deepa rajamani]

Hi,

Is it possible to run MD on a small part of a large protein by defining a
small box region, while using the periodic boundary conditions.
When I try to make a small box by defining the atoms in an index file, the
program complains of difference in number of coordinates between the .gro
file and .top file when generating the .tpr  file. Any suggestions?

Deepa