#load force field

include "loadff.inc"

#load MSF built previously

loadmsf file="step2_solvbox.msf"

#load MD core

loadsetup file="step4_equil_npt.mds"

#tell times information in the file

trjin file="step4_equil_npt.trj"

ts=$timeend-500

tell natom select="iseq 1"

natom1=$natom

tell natom select="iseq 2"

natom2=$natom

#calculate Radial Distribution for ions pair

trjcalc rdf trjfile="step4_equil_npt.trj" cutoff=20.0 binSize=0.05 \

        reference="resn bmi"  target="resn pf6" startpos=1.2 \

        natomref=$natom1 natomtar=$natom2 \

        trjfile="step4_equil.trj" \

        timestart=$ts \

        output="rdf_bmi_pf6.txt"