#protocol params numsteps 20000 #initial config ambercoor ../3mem3mem.crd parmfile ../3mem3mem.top #output params outputname 3mem3mem_min binaryoutput on #force field params paraTypeCharmm off amber yes parameters ../parm94_aby.dat exclude scaled1-4 scnb 2.0 1-4scaling 0.83 switching off switchdist 8.0 cutoff 12.0 pairlistdist 14.0 pairlistsPerCycle 2 margin 0.0 stepspercycle 20 rigidBonds all timestep 0.5 #colvars section colvars on colvarsConfig colVarfile.txt #colvarsInput #dcd file DCDfile 3mem3mem_atombased.dcd DCDfreq 10 #binvelocities 3mem3mem_min.vel temperature 300 ##abf section #source ./Tutorial-ABF/abf-1.8/abf.tcl #abf coordinate distance #abf abf1 90 #abf abf2 59 #abf xiMin 1.45 #abf xiMax 9.00 #abf dxi 0.1