[gmx-developers] data structure in gmx

Fan Hao f.Hao at chem.rug.nl
Wed Jul 2 15:06:43 CEST 2003

Hi, all:
    I have quetions about gmx data structures. I use Gmx3.0.5 code
with G9643a1 force field. I want to get bond, angle and LJ_14 atom pairs
and related parameters so I read these parameters in do_force from
t_topology *top. 
    I am not sure how I can get number of bonds in protein, For each bond,
the sequence number of the two atoms and the related parameters.
The following are my assumptions.
number of bonds:              idef.il[F_BONDS].nr (Maybe F_G96BOND)

sequence number of two atoms in bond i:
     idef.il[F_BONDS].iatoms[i*2-1] and idef.il[F_BONDS].iatoms[i*2]

vdw parameter for atomtype i  if nratt is number of atomtypes in G96:

ideal bond length for bond i:

I think when I use All-bond constraint with G96 FF, I still can have the
bonded and angle atom list but I was confused by the definition of
t_iparams. Does gmx use harmonic for both bond and angle(I don't find
other type in this union)? If I want to have parameter cos(theta0) for
angle i, is the following correct?

I am sorry to provide some boring questions, any hints will be sincerely
appreciated. Thanks a lot in advance!


Hao Fan

More information about the gromacs.org_gmx-developers mailing list