[gmx-users] lincs algorithm

[Lin Zhen]

Dear all,

 I am doing a research on the lincs algorithm for molecular dynamics,
I found  one interesting paper with psedudo code

LINCS: a linear constraint solver for molecular simulations
B. Hess, H. Bekker, H. J. C. Berendsen and J. G. E. M. Fraaije
J. Comp. Chem. 18: 1463-1472 (1997)

and I find the source code in Gromacs. I am trying to do some
modification of the code ( clincs.c), but there are something I am not
sure:

Is B( the constraint matrix ) has demesion k * 3, k is the number of constraints

Matrix M should contain the masses of the particles,  is it 3 by 3 in
the program ?

I am asking this, because I  am trying to calculate BM^(-1)B, but not
sure about the value and dimesion of matrix B and matrix M.

If you can tell me that will be a big help, thank you very much!

-- 
Best Regards!

Jane Zhen Lin