Hi!
The tabulated function is applied to all interactions, both bonded and
non-bonded. The function is initialized in make_gb_table(), and accessed in the
non-bonded kernels the same way as other tabulated functions are accessed. See
GBtab[nnn] in the kernels for more details.
In calc_gb_chainrule() the values of dadx (the derivative of the radii wrt. to
the coordinates), and dvda (the derivative of the potential wrt. to the radii),
which are calculated in the kernels, are simply multiplied together to yield
the total force.
Cheers
/Per
31 mar 2011 kl. 21.09 skrev Chi-cheng Chiu:
Hi,
I have been tracking the code for implicit solvent, i.e. src/mdlib/genborn.c
According to the gromacs paper on implicit solvent, J Comp Chem 31:2593,
2010, the GB force is tabulated in the X = Rij Ci Cj dimension.
However, the tabulated function, which I think is stored in fr-gbtab, is
only used in the function gb_bonds_tab().
I could not find the function of X applied in the calc_gb_chainrule()
function. Does the gbtab applied on dvda and dadx elsewhere? Thanks in
advance!
regards,
Chi-cheng
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