Dear Amber Community!
I am not fully understand the SHAKE algorithm in Amber.
I am wondering how the AMBER implement the SHAKE algorithm,(1) or (2).
(1) Solve the linear equation method.
(2) Using Iteration method to convergence.
If AMBER uses (2),which Iteration strategy does AMBER do, (a) or (b).
(a)
while(not convergent)
for i = 1 to number_of_shake_bonds
shake_correction() //one interation.
endfor
endwhile
(b)
for i = 1 to number_of_shake_bonds
while(not convergent)
shake_correction() //serveral interation until convergence.
endwhile
endfor
which iteration is better?
Could anyone help me! Thank you very much:)
BEST REGARDS
Fu Lin
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Received on Wed Aug 08 2007 - 06:07:45 PDT
