[gmx-users] localized molecular dynamics

[Mark Abraham]

Giacomo Bastianelli wrote:
> Dear users,
> 
> I was wondering if it is possible with gromacs
> to run a MD of a protein just in few residues (let's say a pocket).
> Does it reduce the calculation time for the dynamics?

Not really. Taking that section out of the protein is unlikely to lead 
to a meaningful result, so you have to leave most of the protein for 
context. The most time consuming part of MD is calculating the 
non-bonded interactions, and you'd still have most of those and then 
have to justify that the fragment you held fixed was realistic somehow.

Mark