title                    = MD simulation of 1L3F_uc
;Preprocessor
cpp			 = /lib/cpp
;Directories to include in the topology format
include 		 = -I/home/siva/shankari/forcef
;position restraint for protein
define             = -DPOSRES_UREA
;Run control: A leap-frog algorithm for integrating Newton's equations. 
integrator		 = md
;Total simulation time: 300 ps
;time step in femtoseconds 
dt			 = 0.002
;number of steps
nsteps  		 = 150000
;frequency to write coordinates to output trajectory file
nstxout 		 =500
;frequency to write velocities to output trajectory file
nstvout 		 =500
;frequency to write energies to log file
nstlog  		 = 5000
;frequency to write energies to energy file
nstenergy		 = 500
;frequency to write coordinates to xtc trajectory 
nstxtcout		 = 500
;group(s) to write to xtc trajectory
xtc_grps		 = urea sol
;group(s) to write to energy file 
energygrps		 = urea sol
;Frequency to update the neighbor list (and the long-range forces, 
;when using twin-range cut-off's). 
nstlist 		 = 10
;Make a grid in the box and only check atoms in neighboring grid cells 
;when constructing a new neighbor list every nstlist steps. 
ns_type 		 = grid
;cut-off distance for the short-range neighbor list
rlist			 = 0.9
;treatment of electrostatic interactions
coulombtype		 =PME
rcoulomb		 = 0.9
fourierspacing                =0.12
pme_order                    =4
ewald_rtol                    =1e-5
optimize_fft                  =yes
;treatment of van der waals interactions
rvdw			 = 1.0
;Temperature coupling
tcoupl  		 = berendsen
tc_grps 		 = urea sol   
tau_t			 = 4.0 4.0    
ref_t			 = 300 300  
;Pressure coupling
Pcoupl  		 = berendsen
Pcoupltype                     =  anisotropic
tau_p		 = 5.0 5.0 5.0 5.0 5.0 5.0
compressibility              = 0 0 4.5e-5 0 0 0 
 ref_p		 = 1.0 1.0 1.0 1.0 1.0 1.0 
;Velocity generation
gen_vel 		 = no 
gen_temp		 = 300
gen_seed		 = 173529
;Constrain all bonds
constraints		 = all-bonds
;freeze
;freezegrps               = urea 
;freezedim                = Y Y Y