[gmx-developers] Units in the force field parameter files

David Cerutti dcerutti at mccammon.ucsd.edu
Thu Apr 6 04:29:55 CEST 2006


    I am trying to re-cast the GROMOS-96 forcefield in a different set of 
topology files for my own code to read and work with.  When I see the 
ffgmxbon.itp file, I am not certain what some of the fields mean:

[ bondtypes ]
   ; i    j func        b0          kb
     C    O    1   0.12300     502080.
     C   OM    1   0.12500     418400.

I know the fourth column has units of nanometers for a harmonic bond, but 
I'm not sure about the final column.  It seems to be the spring constant 
in kJ/mol-nm^4, correct?

[ angletypes ]
   ; i    j    k func       th0         cth
    HO   OA    C    1   109.500     397.480
    HO   OA  CH1    1   109.500     397.480

Since I don't see anything but func 1, I'm assuming that the th0 value is 
the equilibrium angle in degrees, about which bending incurs a penalty of 
0.5*cth*(cos(theta) - cos(th0)).

    Next, I just want to make sure that I recall correctly about GROMOS 
(it's been awhile!): the dihedral parameters somehow apply depending only 
on the center two atoms or something, but I forget how.  Can 
someone explain?

    I think that pretty much covers it.  Not too bad, here, but I'm going 
to have to do a bit of extra coding if I want to use GROMOS as an MD 
potential in my code, rather than just something to compute non-bonded 


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