[gmx-users] some questions about the tabulated interaction functions
Mark.Abraham at anu.edu.au
Thu Sep 17 04:32:19 CEST 2009
> Dear GMXers,
> by looking through the manual, I find that the tabluated interaction
> functions seem very flexible for performing MD simulations. But some
> questions puzzle me too much:
> for bonded interactions, as for bonds, angles, dihedrals, the f'(x)
> are the derivations of f(x) respective to x, here x can be considered
> as values of bonds, angles, and dihedrals?
Yes, I suppose so. Check out the manual, sections 4.2.13
> for non-bonded interactions, as for coulomb and LJ, the f'(x) are the
> derivations of f(x) respective to x, here x can be considered as values
> of distance between non-bonded atoms?
Yes, manual section 6.7 makes that pretty clear in equation 6.23
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