AMBER: Dummy Atom Types on both states

From: Ilyas Yildirim <>
Date: Mon, 14 Feb 2005 21:29:03 -0500 (EST)

Dear Amber Developers,

According to pp.134 of the AMBER Manual, Eq. 5 (pp.133) is designed for
having dummy atoms in the perturbed Hamiltonian and 'real' atoms in the
regular Hamiltonian.

Dummy atoms are just atoms (or atom TYPES). They have some parameters too,
except that the non-bonded parameters are set to be zero. Let's say that I
have described a dummy atom, DH, such that the mass, bond length, bond
angle, dihedral angle, and the corresponding force constants of H are used
as the parameters for DH. The nonbonded terms of DH are set to be zero.
(As it is done in David Case's tutorial) And lets say that I have this DH
in both states; namely at state 0 and state 1 of my system. When sander
does the MD simulation, it should see DH as a new atom type, except that
the nonbonded parameters are set to be zero. And during the MD simulation,
is this going to create some singularities, or infinities? At the end, DH
is nothing but another atom type.

I will appreciate if someone can give me a reference on that, or explain
how sander will see the DH atoms. Thanks in advance.

  Ilyas Yildirim
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  -                     -
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Feb 15 2005 - 02:53:01 PST
Custom Search