[gmx-users] structure factor

[Yousung Jung]

How is pbc handled in calculating structure factors (SF) from MD simulation in general? I wrote a small program to compute SF for a box of water given the trajectory obtained from Gromacs, but it suffers from an edge effect (hard-sphere scattering).

Do people (or does Gromacs) calculate radial distribution function (RDF) first with pbc considered, and then fourier transform it to get SF?

Thanks!

Yousung

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