1)generate .psf file:
	cd 1-1-build/
	in vmd using Tk console from Extensions
        set ubq [atomselect top protein] 	 
	$ubq writepdb ubqp.pdb
	
	vmd -dispdev text -e ubq.pgn (using psfgen)
	or using automatic PFS builder within vmd

2) solvate the protein (sphere)
	vmd -dispdev text -e wsphere.tcl
  
   solvate the protein (box)
	package require solvate 	
	solvate ubq.psf ubq.pdb -t 5 -o ubq_wb 	

   cp ubq.pdb ubq.psf ubq_w* ../common	 

3) cd ../1-2-sphere
	parameter file: ubq_ws_eq.conf


4) run simulations
serial: 
	namd2 ubq_ws_eq.conf

ibverbs parallel:
	namd2 +p 4 ubq_ws_eq.conf
	charmrun ++local ++p 20 `which namd2` ubq_ws_eq.conf
	charmrun ++nodelist nodefile ++p 20 -remote-shell shell `which namd2` ubq_ws_eq.conf
	 
MPI parallel:
	mpirun –np/-ppn <procs> -hostfile $PBS_NODEFILE `which namd2`  ubq_ws_eq.conf
