I am trying to run some coarse-grained simulations of an Intrinsically Disordered Protein (IDP) using the Martini force field, and I want to increase the strength of interaction between water and protein. Specifically I want to alter the $\epsilon$ value to change the Lennard-Jones potential calculation at each update:
From my understanding, the potential parameters are stored in this .itp file in the form of an interaction matrix:
[ nonbond_params ] P5 P5 1 4.700000e-01 5.000000e+00 P4 P4 1 4.700000e-01 4.750000e+00 P2 P2 1 4.700000e-01 4.300000e+00 P1 P1 1 4.700000e-01 4.100000e+00 N3 N3 1 4.700000e-01 4.100000e+00 ...
[ nonbond_params ] P5 P5 1 0.24145E-00 0.26027E-02 ; supra attractive SP5 SP5 1 0.10620E-00 0.67132E-03 ; 75supra attractive, s=0.43 P4 P4 1 0.21558E-00 0.23238E-02 ; attractive BP4 BP4 1 0.21558E-00 0.23238E-02 ; attractive SP4 SP4 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 ...
There are no headers so I don't know which value is which, but I imagine the first is $\sigma$ and the second is $\epsilon$ ? I also can't find what each of the letters represents except for some definitions in the 2008 Martini paper.
Do I need to write a parser in python that modifies these column values for the relevant interaction pairs? Or is there an easier way to do this?: