This tutorial will show you how to reproduce the method in the recent
White et al. water AIMD paper (White, Knight, Hocky, & Voth, 2017). The
goal of the method is to minimally bias a water simulation to match a
reference RDF. We will first convert a reference RDF into a set of
reference scalar coordination number moments. Then, an NVT simulation
is run to find a minimal bias which causes the coordination numbers to
match their reference values. It won’t be covered here, but the bias
can then be used to run NVE simulations or in conjunctino with other
free-energy methods. This tutorial will use classical simulations in
Lammps instead of AIMD in CP2K so that results can be obtained in a
reasonable amount of time.
I’ve decided to start summarizing literature topics on areas I’m
interested in on my blog. I’m starting with peptide self-assembly of
diphenylalanine. This is a very incomplete survey of work on it.
One of the most common self-assembling motifs is diphenylalanine, or
FF in the amino acid code alphabet. FF is the shortest self-assembling
peptide sequence. It is stable up to 100°C and
150°C with dry heating (Sedman, Adler-Abramovich, Allen, Gazit, & Tendler, 2006), it has a Young’s modulous of 19 GPa (somewhere between human bone
and concrete) (Kol et al., 2005) and is stable in harsh
solvents such as acetone and alcohol (Adler-Abramovich et al., 2006). FF, or some variation of it, is thought to become an important
building block in future biological applications (Yan, Zhu, & Li, 2010).
Metadynamics is a way of overcoming energetic barriers in molecular
simulation (Laio & Parrinello, 2002). It’s part of a class of algorithms
that focus on making rare-events more frequent in simulations. It’s
been getting quite popular: it even has it’s own wikipedia
page. One problem with the
method is that it has systematic errors at boundaries and this was
recently fixed via a method introduced by Michael McGovern and Juan de
Pablo (McGovern & de Pablo, 2013). I’m recording the equations here in,
since I use an implementation of it and the derivatives weren’t shown
in the manuscript, which are necessary for the implementation.