[gmx-users] Hydrogen Database Format - Control Atoms

Travis Craddock tcraddoc at phys.ualberta.ca
Thu Jul 24 17:58:22 CEST 2008

Hello all,

In the Gromacs Manual 3.3 the format for the hydrogen database is given in
section 5.5.2.  It follows that the format for each addition is:

number of H atoms
way of adding the H atom
name of the H atom
3 or 4 control atoms

In regards to the 3 or 4 control atoms the manual states:

Three or four control atoms (i,j,k,l), where the first always is the atom to
which the H atoms are connected. The other two or three depend on the code
selected (for water there is only one control atom).

What does it mean "The other two or three depend on the code selected", and
how are they determined?  This is not elaborated in the manual.


Travis Craddock
Department of Physics         
University of Alberta

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