[gmx-users] Position restricted md

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Tue Oct 23 10:32:07 CEST 2007

  I understand.Thank you for the comparative analysis.

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 
>>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 
>>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?
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