[gmx-users] implicit solvent GB force table

Per Larsson per.larsson at sbc.su.se
Thu Mar 31 21:17:48 CEST 2011


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.


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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