I understand.Thank you for the comparative analysis.
sarbani
On Tue, 23 Oct 2007 Mark Abraham wrote :
>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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