source ww_nearest.tcl


# initial trajectory
set trajpsf small_pept.psf
set trajdcd neat_every100.dcd

#load the full trajectory
set mol [mol new $trajpsf waitfor all]
mol addfile $trajdcd waitfor all

#define some variables
set newtrajname trimmed_traj
set macromol "(protein)"
set what "(water)" 
set cutoff 5
set howmany 10

#generate a trimmed trajectory, i.e., protein or water within $cutoff of
ww_nearest $macromol $what  $cutoff $howmany $newtrajname $mol


quit