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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