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
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