In
the past step of my project I used the espresso command to make the
neighbor list of particles to see if they made special structures. The
command was:
set nbhood [analyze nbhood idParticle cutOffRadious]
In condensed material simulations I figured it out that lots of complementary bases would interact which a single base that is different from the physics of base pair(A_T C_G) interactions. Now I dont know how to include it in Integration by Espresso. Usually in the tcl program we define the interactions among the types of particles. But now I should look at the particles at every step and then decide which particles interact with each other.
Thanks,Mohammad