AMBER Archive (2007)

Subject: AMBER: about shake

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Tue Aug 07 2007 - 20:36:59 CDT

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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