Looking for info on hamiltonians for proteins.

Andrew Dalke dalke at ks.uiuc.edu
Tue Aug 22 22:25:01 EST 1995


> What I would like try to do is integrate  the hamiltonian of some molecule
>using a symplectic numerical integrator

A typical molecular mechanics Hamiltonian has many terms, usually for 1, 2, 3,
and 4 bodies.  There are any number of books which describe them, for instance
McCammon and Harvey, "Dynamics of proteins and nucleic acids"
              ___          2           ___                   2
    V = (1/2) \  ( K (b-b )  ) + (1/2) \  (K (theta - theta )  )  +
              /__   b    0             /__  theta          0
              bonds                   angles


             ___
       (1/2) \  ( K  (1+cos[n phi - delta)]) +
             /__   phi
           dihedrals


       ___  [    A        C      q1 q2     ]
       \    [   ---   -  ---  +  -----     ]
       /__  [   r^12     r^6      D r      ]
      nonbonded   
      pairs


> What I would like try to do is integrate  the hamiltonian of some molecule 
> using a symplectic numerical integrator running on several loosely coupled
> processors.

  You might want to take a look at our program 'namd'.  Information about it is
on the web at http://www.ks.uiuc.edu/Research/namd .  The program is designed
for workstation clusters, which is about as loosly coupled as you can get.  It
is also designed to be used by others, so there is complete source code
documentation (the "programmer's maual") as well as commented C++ source code
which is freely available and for free from our ftp site (ftp.ks.uiuc.edu in
/pub/mdscope/namd).  Plus, we plan to experiment with different simpletic
integrators - though only a couple Verlet methods are there now.
  Also, there is a section in the the documentation describing (in glourious
LaTeX equations) the different terms of the Hamiltonian, and differentiating
them to get the force terms as well.  BTW, the documentation is in Postscript.

						Andrew Dalke
						dalke at ks.uiuc.edu




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