title           	=  MD of a simulation system including protein solvent and ions
cpp                 =  /lib/cpp	  				 


; run parameters
integrator      =       md		    
tinit           =  		0       	
dt              =       0.002		
nsteps          =       5000000		


; initial velocity generation
gen_vel		= no		; continuation from NPT equil


; physical parameters

; pressure coupling
nstpcouple			= 1
pcoupl              = Parrinello-Rahman     
pcoupltype          = isotropic             
tau_p               = 2.5 					
compressibility     = 4.5E-5 
ref_p               = 1
  
; temperature coupling
tcoupl              = nose-hoover               
ref_t               = 298.0  	298.0    	    
tau_t               = 0.5    	0.5       	    
tc_grps             = Protein_Het_vedani_wat 	SOL_ION	    
nsttcouple	        = 1 			    


; output parameter  
nstxout-compressed  	=  2500		
compressed-x-precision 	=  1000		 	
nstenergy           	=  2500		  	
nstxout             	=  5000000 		
nstvout             	=  5000000		
nstfout             	=  5000000		
nstlog              	=  5000000		


; neighbor search
nstlist             	=  10			
cutoff-scheme       	=  verlet	 	
verlet-buffer-tolerance =  0.005		
ns_type             	=  grid			
pbc                 	=  xyz	        	
rcoulomb            	=  1.1          	
rvdw                	=  1.1          	
vdw-modifier            = Potential-switch	
rvdw-switch		        = 1.05			


; electrostatics 
coulombtype         =  PME     
pme_order           =  4       
fourierspacing      =  0.12    
ewald_rtol          =  1e-5    
vdwtype             =  cut-off 


; bond parameters
continuation			= yes			
constraints             = h-bonds  		
constraint_algorithm    = lincs 		
lincs_iter              = 1          	
lincs_order             = 4          	


; COM motion removal
nstcomm   			= 1000     	
comm_mode 			= Linear    
comm_grps 			= System  	
refcoord_scaling 	= com