[gmx-developers] data structure in gmx
f.Hao at chem.rug.nl
Wed Jul 2 15:06:43 CEST 2003
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
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!
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