AMBER Archive (2009)
Subject: [AMBER] g(r) extrapolation
From: Lorenzo Gontrani (l.gontrani_at_caspur.it)
Date: Wed Feb 18 2009 - 09:16:26 CST
Dear Amber users, I am collaborating with a group of X-Ray
They asked me to try to calculate the structure factors of some
molecular liquids through MD simulations..
I obtained a couple of AMBER trajectories and I calculated the RDF
with ptraj, and then calculated the structure factor by Fourier
transformation with a in-house code.
The fit with experimental data is very good at intramolecular
distances (high k values), but gets worser at high distance..I guess
that there could be some problems with the finite-size effects, since
ptraj RDF are (obviously..) calculated within the hypothesis of
minimum image convention, so that the maximum r value is half the box
Does any body have suggestions on how to estimate the g(r) outside
the box and/or suggest me some papers on this issue?
Thanks a lot
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