Concentration Dependency

1. Prepare a concentration file for input with this little perl script

   	  $ perl -e '$c=1e-06; do {print "$c\t$c\n"; $c*=1.5;} while $c<0.2' > concfile
   

2. Compute the MFE, the ensemble properties and the concentration dependency of hybridization.

   	  $ RNAcofold -f concfile < t.seq > t.out
   

3. Look at the generated output

   [...]
   Free Energies:
   AB           AA           BB           A             B
   -17.223943   -17.223943   -17.223943   -6.808189     -6.808189
   Initial concentrations          relative Equilibrium concentrations
   A            B            AB           AA          BB          A           B
   0.0001       1e-09        0.00000      0.03069     0.00000     0.93860     0.00001

The five different free energies were printed out first, followed by a list of all the equilibrium concentrations, where the first two columns denote the initial (absolute) concentrations of molecules $A$ and $B$, respectively. The next five columns denote the equilibrium concentrations of dimers and monomers, relative to the total particle number. (Hence, the concentrations don't add up to one, except in the case where no dimers are built - if you want to know the fraction of particles in a dimer, you have to take the relative dimer concentrations times 2).
Since there are 7 columns in this output, it is not trivial to visualize the results. We usually try to keep the initial concentration of one molecule constant to avoid the necessity of 3D plots. As an example we show the following plot of $t.seq$. Now we use some commandline tools to render our plot. We use tail -n +11 to show all lines starting with line 11 (1-10 are cut) and pipe it into an awk command, which removes the first column from our input and write it to xm.plot. Then we open xmgrace -nxy and tell it to read data file in X Y1 Y2 ... format.

	  $ tail -n +11 t.out | awk '{$1="" } 1' > xm.plot
	  $ xmgrace -nxy xm.plot