Hi,
On Apr 11, 2007, at 7:26 AM, Priya Chandran wrote:
2. Is minimisation in GROMACS only used as a precursor to the md-
simulation to remove bad contacts, or can we also use it
effectively to minimize a raw modelled ab-initio structure.?
Well, technically you can of course use it, but any energy
minimization algorithm will only take you to a close local minimum in
the energy (=enthalpy) landscape.
If you want your model to get closer to the native state you need
refinement, and that's way more complicated. Search the literature
for techniques like simulated annealing, Replica-exchange molecular
dynamics, etc.
Cheers,
Erik
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