sarbani chattopadhyay wrote:
yes , I had gone through the manual, but is that all? I mean to say
that even if the protein
suffers from high solvent forces (though the energy minimisation can be
done over the
whole system ie protein in solvated state) that may not pose much of a
problem , in case we
simulate for sufficiently long time.
I am sorry if I understood wrong.
What will converge to an equilibrium ensemble faster, a structure that
started off physical, had its solvent relaxed while it was under
position restraints, and then relaxed itself without the constraints, or
one that was kicked around violently by the initial solvent?
Mark
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