[gmx-users] Position restricted md

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 23 10:22:17 CEST 2007

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?


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