View source for Foward Flux Sampling in MD++

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Forward Flux Sampling of Rare Events in MD++</STRONG></font></P>
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<P ALIGN="CENTER"><STRONG>Seunghwa Ryu and Wei Cai</STRONG></P>
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This tutorial describes how to use Forward Flux Sampling (FFS) algorithm in MD++ to sample rare events (such as nucleation).  The theoretical background is published in 

Rosalind J. Allen, Daan Frenkel, and Pieter Rein ten Wolde, Simulating rare events in equilibrium or nonequilibrium stochastic systems, ''Journal of Chemical Physics'', '''124''', 024102 (2006).
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==Download files==

First, you need to install MD++ on your computer by following the instructions on [[MD++_Manuals | MD++ Manuals]].

Second, copy files ??? and ??? to your input file directory of MD++.  You can do so by the following commands (assuming you have installed MD++ in <tt>~/Codes/MD++</tt>).

<pre>
 export MDPP=~/Codes/MD++
 mkdir -p ${MDPP}/scripts/work/melting
 cd ${MDPP}/scripts/work/melting
 wget ??? -O ???
 wget ??? -O ???
</pre>

==Compile excutable file==

In this tutorial, we will study homogeneous nucleation of crystal from Si melt.  Si will be modelled by the SW potential.  The MD++ executable with SW potential can be compiled by the following command (on wcr.stanford.edu).

For example, you can compile <tt>sworig</tt> by typing
<pre>
 cd ${MDPP}
 make sw build=R SYS=wcr
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If compilation is successful, this will create binary file <tt>sw_wcr</tt> file in your <tt>${MDPP}/bin</tt> directory.

Please contact <tt>shryu@stanford.edu</tt> if you have further questions.


==Run simulations==



==Analyse data==

Nucleation rate of embryonic crystals.

Survival probability for the embryonic crystal to grow to larger (stable) size.