AMBER: about shake

From: linfu <>
Date: Wed, 8 Aug 2007 09:36:59 +0800

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).
    while(not convergent)

         for i = 1 to number_of_shake_bonds
            shake_correction() //one interation.

     for i = 1 to number_of_shake_bonds

         while(not convergent)
            shake_correction() //serveral interation until convergence.

which iteration is better?

Could anyone help me! Thank you very much:)

Fu Lin

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Aug 08 2007 - 06:07:45 PDT
Custom Search