[gmx-users] localized molecular dynamics

Mark Abraham Mark.Abraham at anu.edu.au
Wed Dec 13 14:48:01 CET 2006

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.


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